Clues to the solution of this problem:
Me, 7-26-08: "I'm bringing it up again because I don't know that it is a carb problem."
Me, 7-27-08: "The choke has no effect on performance when the bike is flubbing. I've tried opening the choke at the moment the flub starts. Also tried running the bike on choke the whole time."
Me, 7-27-08: "Coil or ignition module?"
Me, 7-27-08: "Unfortunately, it does it hot or cold."
Me, 7-27-08: "Nearly yanked the carbs again yesterday but had a hunch it might be electrical. Now I'm thinking it almost has to be electrical."
RVAVMAX, 7-27-08: "I would guess that it would have to be somewhere in the ignition though... Hopefully you won't have to do much digging to find it."
Me, 7-27-08: "Will a coil crap out only at high revs?"
gleno, 7-28-08: "I would say the problem is electrical. I've looked at your posts to try to understand the sequence of events leading up to the problem."
gleno, 7-28-08: "4) A Dud coil. Check resistances."
richwrench, 8-01-08: "take apart every single electrical connector you can find, spray with contact cleaner, apply with di-electric grease & re-assemble."
me, 8-12-08: "Bike flubbed sporatically today again and then recovered. Got to be an electrical issue, like TCI box.... "
me, 8-23-08: "Took a ride today and the bike wanted to sputter and cough regardless of RPM. This makes me think the problem is not a fuel/carb issue."
me, 8-23-08: "#1 and #3 coils and caps are stock but #1 and #3 coil wires are some non-OEM yellow wires that say "radio supression" on them.... (these are the two I replaced on 9-22-08)
me, 8-23-08: "I guess I could try swapping #2 coil to #1's spot and see what happens. I can see that the spark color is a little different between the stock coil/wires and the others."
KJShover, 8-23-08: "I may have missed this in your other thread. I agree with mark. What color is your spark? Have you tried different plug wires? If the PO didn't put them on right or somthing may have come loose. I had a similar situation on my Venture, and it turned out to be somewhere in the coils or plug wires. I cant tell ya which cause I swapped them both out at the same time. but the problem went away."
ssnsltd, 8-24-08: "I got new (used 4k) coils and wires to try since 3 of my coils were cracked I thought that might be it."
me, 8-24-08: "I swapped #3 coil with #1. Still seems to be a problem so I don't think it's the coil." (doh! bad logic, here - if 1 and 3 are both bad, this test is useless)
jedi, 8-30-08: "When you swapped coil, did that include HT lead & plug ? If not, could be the issue"
maleko89, 9-03-08: "My question is has anybody ever have an early model coil go out but only affect one cylinder? In my case, I dropped two cylinders as expected. I don't know, it might be worthwhile to test all four cylinders but would test #2 or #4 first."
dave741, 9-04-08: "i dont know if it relates but i can tell you 4sure that at least in cars half of your coil can go bad "
me, 9-04-08: "That's a good idea. Why not connect the voltmeter to the 12v wires feeding the coils? Then take the bike out and see if there is an input voltage problem..... that's another test I can do to help eliminate electrical as the culprit...."
me, 9-05-08: "What I found did not surprise me. The timing light indicates that the bike is getting good spark." (apparently the coil or coils crapped out more on the mid-range than idle)
me, 9-20-08: "It's not a carb problem, as Mark ran my carbs on his bike and they were fine."
me, 9-21-08: "Question: Will the bike run with the boost sensor and vboost controller unit disconnected? I don't remember if I have tried that. Both devices connect to the wiring harness. Yes I'd loose boost but if the bike doesn't sputter, then I've found the problem. If it still sputters with those devices disconnected, I will swap ig. coils. If it still sputters, I will swap pickups. Still sputters then I will have to assume wiring harness/connector problems and/or ign. module." (I removed the boost sensor connector and VBoost module connector, which did not solve the problem. This led me directly to the next step, swapping out the rear coils.)
Solution:
me, 9-22-08: "Replaced the 2 rear ignition coils/wires/caps with the 2001 (cracked) set from Pinwall and the bike took off without a hitch. I'll ride it tomorrow to make sure, but I think it had to be something with one or more of the rear coils."
I think I'm going to agree with Mark about the coils: I think they all are reasonably within spec; I think it's the connection and/or resistance between the coil and the plug that is the problem, and I think it could be on one or both of the coils. I'll know when I get around to putting the stock wires/caps on coils I just removed.