Hi,
Yep, I was using the 145 main (Mikuni brand) at my 5280' altitude (and higher of course when I ride up the canyons of Colorado).
I've gone as low as 142.5 for mains also, but with no noticeable difference compared to the 145's.
As for the PAJ 2's, I currently run 180 Mikunis. The bike runs much crisper in the midrange with that setup. Seems you want to keep the PAJ 2's large to keep the mid from running too rich. That setup makes for a really crisp midrange.
I think with the Cobra's, you have less 'suction' and scavenging effect in the exhaust system due to no crossover tubing or collector pipe built in. What does this cause? Well, I'm thinking it may cause a less efficient condition because you don't have the suction to pull out the exhaust from the cylinders once the exhaust valves open.
Does this make the bike richer or leaner? I'm not too sure. I think it may simply make the bike produce less power. I don't think a lot of the efficiency loss of that exhaust system can be cured by going richer or leaner.
My thoughts are this;
I think going leaner with the Cobra's or any exhaust, will produce more power. Reason being, the stock setup is set a bit rich for safety. The factory puts the same jetting for 49 states regardless of altitude. So, I think they run rich and even when actually at sea level, the density altitude is always quite a bit higher. That would mean when you're actually sitting on a bike right by the ocean's side, the density altitude may show that it's the equivalent of being 1000' in the air.
So, Cobra's probably like a bit of 'lean' tuning. This means smaller mains, and larger PAJ 2's for the midrange. BUT, the stock exhaust system benefits with this also.
Here's the scenario I'm thinking:
1) stock system not tuned compared to Cobra's not tuned (loss of quite a bit of power due to less efficiency, due to less scavenging effect from Cobra's).
2) stock system not tuned compared to Cobra's 'tuned' for better running (you'd experience less of a power difference comparing the 2 systems. Maybe Cobra would only see a 5-6hp difference in loss compared to the normal 10hp difference).
3) stock system 'tuned' compared to Cobra's 'tuned' (you're going to see that both systems tuned will make more power compared to un-tuned setups, but the Cobra's will still never come close to stock and you'd be back to the 10hp difference *loss with the Cobra's).
For all running, I'd try and go leaner on the PAJ 2 and get it as crisp as possible in the midrange. Too lean of course and you cross over the crispness peak and you may experience jerky throttle in the midrange when cruising.
Vinnie