96 sitting for 4 + years.

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So I found the problem....the exhaust cam on 1 and 3 is 180 degrees from it should be a TDC.
Are you vertifying that in the Yamaha manual?
I would call the guy and ask him to explain to you exactly what he did when he said he tried to adjust the valves.
Dont be rude or blame him for ****. Just explain to him your trying to get it running again and need his help in figuring out Exactly what was taken apart, move, adjusted, and breathed on.
That would get you a lot further ahead than taring down the motor.
 
So I found the problem....the exhaust cam on 1 and 3 is 180 degrees from it should be a TDC.
The query 82nd Cowboy posited is a reasonable one to ask-of the prior owner. However, at this point, to protect your investment, I would give serious consideration to determining how to proceed, based upon his reply, and also whether you see new gaskets evident for the case covers, and the heads. You may-need to consider removing the engine and spending for a complete gasket set, to split the cases if you want to search for any-other botched work of a more-serious nature. Yes, a pain to do it, but how much of an inconvenience would it be to replace a blown engine, because of improperly-clearanced journals, not-to-spec torque on the conn rods, a loose clutch basket, or any of the other possible things to go-wrong in a build he or someone-else may-have done? Obviously, the prior owner slapped-it back-together, couldn't get it operable, and sold it "as-is," as-in "prolly needs a tuneup, carbs adjusted, or sump'in." I hope that your purchase price was for a non-runner! My usual maximum price I'm willing to-pay for a non-runner is $500, only with paperwork, and complete and together. A Basket Case, half of that, unless it's got a bunch of parts that could be sold separately, like aftermarket wheels, a full performance exhaust in good-shape (No Cobras!), the OEM sissy bar/luggage rack, a Stage 7 kit, etc. Actually, there is a market for the 4/4 Cobras, as some people value appearance over performance, even if it's less-than stock. I'm merely expressing my predilection for an exhaust which works at-least as-well as the OEM. But, hey, if it's all stuff being parted-out, a Cobra can sell.

I think you're very-lucky you didn't end-up with an interference between valves and your cylinder heads.

Many years-ago: One of my friends gave me an XS-650 which was very-rough. He got it because it was abandoned at a rental property by a former tenant, who left no forwarding address. The engine was together and complete, not seized but the gas tank was rust-perforated. I used a remote gas tank to be able to start it up, but it was noisy, as-in hammer-on-anvil noisy. I immediately shut it down, it was running on one cylinder. I tried a compression test, one had zero. Pulling the valve cover showed that somehow, the valve keepers spit-out on one valve. I took a look at the piston crown, and didn't see anything fatal. The valve stem of the valve where there were the errant valve keepers wasn't bent, a fortunate circumstance. I wasn't looking to do anything but to get the bike running, to-sell. I put it back together and sold it and a KZ 1000 LTD to two guys from the U.K. who were collecting an ISO container full of USA motorcycles to ship-back home for refurbishment and for-sale. I got them a Honda DOHC 750F from a friend, into the container it went. I heard that when they tried to go to the port (Port Everglades FL) they were unable to provide proper paperwork on one bike in the container, and that meant the entire container was emptied and inventoried against their shipment bill of lading. They almost missed the ship's sailing. Evidently, at the time, it was cheaper to come to the USA for used bikes, and to ship 'em back to the U.K. and to repair them for-sale, than to try to buy used bikes there. They did that a couple times that I know-of and I didn't hear about them after that.
 
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thanks for all of the advice. Locating the guy who did all of the work is going to be difficult, he moved to Europe somewhere with the Navy. Is there any reason that the cam shaft would be turned the way it is? all of the manuals say it should be the other way, but manuals have been wrong before. The guys dad says he only worked on the valves and clutch, which also is not working. I paid $200 for the bike and a Grazia lift table. I figure the table is worth at least that much. There’s one other mod on the bike that I need to figure out too. There is a toggle switch above the kill switch that I don’t what it does, seems to go to the Vboost?? Maybe?
 
How-many miles are showing on the odometer, and is it hooked-up?

Well, you bought it at the right price, assuming that you can make it operable w/o dropping several grand on it. Even if you did, and that was the sum-total of your expenses, assuming that you were able to use it reliably from that point for a few years, you'd be breaking-even, in my accounting. "All he worked-on were the valves and clutch... ." and neither of those areas is currently functional? Do you have the skills to dismantle the engine, and to re-build it, after checking things-out? You could bet big, and just remove, inspect, and replace the camshafts and the clutch basket, and pray that this ham-fisted know-enough to-be dangerous shadetree mechanic didn't split the cases and molest the crankshaft and the gearbox.

As I suggested before, at this point, and working from a point of not-much confirmation as-to the extent of damage the prior owner has done in his "work," for my own peace of mind, I think I'd be in-favor of an engine removal, teardown, and re-assembly. This would also give you the ability to check the transmission, possibly getting it undercut, and re-assembly with correct torque values used, and inventorying things like 'all the parts are where they're supposed to-be.' Also do the oil system O-ring replacement, contact Sean Morley for his upgrade kit for the oil pump & pick-up, cheap insurance that your bike's engine is properly-lubricated. Since you have room for the worktable, I assume that you can use that as a disassembly area to tear-down/re-assemble the engine. Just take the engineless bike off the lift, and wheel it into a corner somewhere.

BTW, what does the inside of the gas tank appear to-be? The bottom and sides should be shiny-bright inside. If they're not, add a tank removal and cleaning to your maintenance list. Plenty of threads about how to do that. I like using 6% or > concentration of vinegar, just be-sure to remove the fuel reserve sender and install a blank-off plate in-place of it, as the potmetal it's made-of reacts poorly to immersion in the vinegar.

The switch is probably something to open the VBoost at a different rpm than the OEM setting. How-many switch positions are there? See if there are any extra electrical boxes added to the round connector under the left scoop. The round connector is for the VBoost connection. If you find something wired-in, post a pic and we can probably I.D. the manufacturer for you.

You really did pick that bike up at the right price, now, some additional $ on your part to check things out, and to ensure it's re-assembled properly (the engine and whatever-else you may discover) you can end-up with a ride for not a lot of $$. Personally, based upon what you've found, I'd go through all areas of that bike: engine, suspension, electrical (have you done the crimp fix yet?), lighting, brakes (a #1 priority to check-out, given what inept mechanical work you have already found), to ensure that something he did incorrectly isn't going to catastrophically-fail and cause you to eat the tarmac.

If you're not-up to the disassembly, it's < 500 miles to CaptainKyle's place in TN if you wanted to bring him the engine. To reach him: [email protected] That's < $100 in gas, round-trip if you get 25 mpg, and an 8 hr trip, one-way I estimate.

Something I found:
 
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I just finished my 1976 GL1000, and needed a winter project. Didn’t expect this to be the project, but now it is. I have not torn an engine all the way down since high school, that was a VW, but I have the tools and time. I’ll start with the cam shaft, valves and clutch, then go from there.
 
I have checked the electrical, all the lights work, brakes work but need to be rebuilt, forks leak, so they will need to be done. All of the gauges work as well as the cooling fan, tested it with direct connection to battery. What is the ‘Crimp Fix’ ?
 
I'm a great believer of 'if it ain't broke don't fix it'.

I would be inclined to remove the cams and re-install them then measure and adjust the valve clearances if necessary.
Do a cylinder leakage check and see what readings you get.
 
Although I'm normally of the same mind as MaxMidnight, I'm not sure I'd go that route in this case. With pretty much everything being an unknown with this bike and being as you've already gone this far, I'd go ahead and bite the bullet and go all the way.

If your luck runs anything like mine, you'd get the cams done, valve lash set, get it all back together and find out that something else has to be redone and it all comes back apart anyway.

Edit to add: My point being that somebody has obviously already been in there and not done a decent job. (And that's putting it kindly.)

So how far did he really go? What else has he screwed up?

You don't know.

So I'd definitely be taking a look at all of it just to be on the safe side if nothing else.
 
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One thing nobody has answered is there in any instance a reason why the exhaust cam shaft would be turned the way it is? I'm going to check everything once I get into it, but just wondering if anyone has ever heard or seen anything like this.
 
Sure, it's called a FXXX-Up.

There's a possibility he just 'did' the cams and the clutch, but considering that the engine could be scrap from something-else he 'did,' I think the wise thing to-do is to remove it, disaassemble it, and completely go-through it. As I mentioned, consider an undercut gearbox, and Sean Morley's oil pump fix. The former makes shifting easier, avoids the second-gear failure so-common on these bikes, and the latter will allow it to-live, because popping out the oil system O-ring can cause oil starvation and a scrapped engine. Take a really-close look at the shift forks and the shift drum, those are pieces that probably should be replaced as you've split the cases. Yes, it's $ but it's going to take care of things known to be points of concern when an engine is abused or has a lot of miles on it, or has been in an accident.
 
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maybe when he was doing the valves he didn't have the correct tool to replace shims, so took out the camshafts to replace any shims and simply put them back wrong,
as it started but ran rough when you first got it, it should start and run ok with the cams in the correct position, I think it's worth a try before complete strip down
 
maybe when he was doing the valves he didn't have the correct tool to replace shims, so took out the camshafts to replace any shims and simply put them back wrong,
as it started but ran rough when you first got it, it should start and run ok with the cams in the correct position, I think it's worth a try before complete strip down
"You're betting the engine on-that!" Sure, try to get lucky. End-up unlucky. The two things the guy or his family admitted to touching, you said, "both are fXXX-ed up." With the use some of us give our bikes, at this point in the brief history of attempted 'repairs,' it's more-than an engine you're putting at-risk. I suggest taking out a huge term life insurance benefit policy. That way, if something happens, someone's gonna be well-off.

I saw you said, "a winter project, I'm taking it down completely," Given what you've found, in the interests of self-preservation, follow that plan. Brakes too. The clutch and front brake master cylinders aren't that-expensive, and don't forget the clutch slave cylinder. Front SS brake lines, HH pads, and you should be good to-go.

Since you already did a GW Honda, you know when you rebuild the front end, not to-use rusted downtubes and just replacing the fork seals, if they're pitted, it's time for replacement. Contact Forking by Frank for replacement downtubes. Much cheaper than the OEM ones.

Sounds like you'll spend some $$ to fix things, but when you're done, it should be reliable and safe, two things sadly lacking due-to ineptitude of the prior owner.

The orange lozenge under the left scoop is indeed a variable operation add-on module for the VBoost. You won't be able to do anything w/it until the bike's operating properly.
 
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no not 'betting on it' but he said it fired straight up but ran rough so it might be alright with the cams in correct position, if any damage was going to happen as a result of running it would have had a good chance to happen with that first fire up, why is is not worth trying to fire it up with things in correct positions
 
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