Mikuni Jet Issue ?

OK I will try adjusting the air screws. Is is also possible that I will need to pull the tops off of the cards and sync then that way or should I do the air screws first ?

Take care to check the need and seat valve assembly inside the carbs. If there is a seat that is all clogged up, that cylinder will be starved of fuel.. might run fine at idle but misfire at higher RPMs.

What should be the starting point for the air screws with my current setup ? K&N pods and a Vance and Hines 4 into 1 pipe with no baffle ?

1½ turns out from lightly seated.

Good Fortune!

I set all 4 air screws to 1 and 1/2 turns out. Warmed the bike up and had it idling just over 1,000 rpms. Did some turning of the screws while listening to the engine and watching the tach for highest rpm. After getting them adjusted and letting the bike run for a few minutes, I pulled the plugs and the #1 plug is starting to turn a greyish color. THe #3 plug is greyish. The #2 and #4 plugs are still sotty. I will continue to adjust those 2 air screws to see if I can get those plugs to change also.

If not already doing so, it's a good idea to run an electric fan blowing air over the engine during the carb tuning process while the bike is sitting there idling.
This is to keep the engine from over-heating.

Good Fortune!

I finally got back to working on this. I do keep a fan cooling the engine while I am making adjustments to the carbs. I have all 4 air screws turned to the higher idle, but I do not see any fluid being pulled into the tubes on the Motion Pro carb tuning tool on the #2 and #4 cyclinders. I sprayed water on the pipes and all 4 sizzle and then evaporates. Any idea what could cause 2 cyclinders to not have any suction and the other 2 not to have any ?

If I read your question right, two have more vacuum than the other two. Then you need to adjust the slide height to change the vacuum so they are the same on all 4. This is the Dynamic Running Sync that the carb sticks/ manometer is for, or vacuum gauges. All 4 should pull the same vacuum if adjusted correctly, and everything else correct.