Mod stock timing plate (free) or AM plate, dual stage reeds, and suspension. Never said what your budget is? Better off waiting till winter to get it ported now, and that should depend on how much life is left in the cyls.
Pull the flywheel with proper puller, not 3 jaw. Clean rust off poles of stator, inside of flywheel, and timing "nubs" on outside of Fwheel. Set pickup gap .018"
Tors delete with idle screws? Try setting idle a little higher with screws or cable. X2 on sync. Could try air screw 1/8 turn or less at a time. I actually adjusted mine 1/8 or less to cure a little hesitation at 1/4 - 1/2 throttle. Tho still hard to start if its been sitting, thinking of trying 30p
Why not just get a Clymers? Or if you're cheep download a manual. or go here: http://www.bikebandit.com/houseofmotorcycles/2000-yamaha-banshee-350-yfz350m/o/m145962
for parts diagram.
http://lmgtfy.com/?q=2+stroke+squish+test
1) Who the fuck told you that?
3) It's the measurement of clearance between piston and head/dome at TDC. http://lmgtfy.com/?q=2+stroke+squish+test
Unless you are way up in elevation, what you have is what you have. IF you start doing bolt on mods then you will get some increase. More air in or out requires jetting changes.
Try cleaning the carbs. While you have it apart see what jets are in it. Trinity didn't give you a ballpark to start at?
BTW, what happened to trinity as a sponsor?