Best mods imo are
Larger head studs as mentioned above.......Could even get the head O-ringed
V-force reeds V2's if possible
Big volume pipe
Get a TM38 off an 88+ and have it reworked/bored (PM me if you need info)....I'd avoid the Lectron imo but that's just me.
Tig weld the hub on the flywheel.......3 small welds around the center hub....Lots of info on that.

Personally I'd keep the stock airbox but do the mod to allow the use of a clamp on filter....SB designs used to make them,not sure if he still does.
If you are going to do a trailport with those other things you should have a reliable 500 that has more than enough go.

Just my .02....Welcome to the board...