Duke, leave the K&N’s on, leave the 4-1 on, check &, if required, adjust the float heights!!
You say the carbs are well balanced & ign set correctly Good
.
Now pick up yer ‘Yellow pages’ & find a competent Dyno shop.
Tell them you have just rebuilt & have new rings fitted, they can ‘run it in’ on the dyno.
Get them to check and set up your fueling, it IS gonna be all over the place.
It should cost you around £60 - £70
Obviously more should parts be required.
Whislt its on the dyno, any other issues should become apparent ... As Harry said, a coil breaking down ?????
Or simply carry on with tank off, carbs off, filters off, exhaust off. Change this , change that .. oh , it might be this !! exhaust on, filters on, carbs on, tank on , Know what I’m saying mate,
how long is all that going to take you.
BTW, a 4-1 exhaust is one of the best set ups you can get, (actually it’s a 4 - 2 - 1 but now I’m being picky)
The reason being, the pulses from each exhaust stroke helps to pull the next one .. .. and so the cycle continues.