Littlebus,
Back up a few steps.
1. Your air filter and intake must have a good seal. Go there first.
2.Make sure your "choke" plunger has a good seal.(o-rings)
3.Pull your spark plug see what it looks like.
4.You need a 150~165 main for a Yoshi. But you must know who made the jet you installed. Some brands use hole size and some use flow rate for sizing. Your air screw only affects idle.
I have yet to see a stock bore/cam/carb 400 need a larger low speed jet.
It is possible you got some trash in the idle/low speed carb circiuts when you replaced the main hance the poor idle/low speed performance.
PS. ASE double master and EVT cert. I still get stumped once in a while.
I am running a dyno jet kit, I cleaned the carb out very well when I had it off the bike so im sure there is no crap in it, a/f is on tight, and choke o-rings are good.