Noice! Welcome Smorkmo, glad ta have you and your experience here - 1500 miles is no small amount given there was a winter in there
You defo need to get a camera as my curiosity is insufferable... ask anyone whom tries to get away w/o posting pics
My suggestions not unique and you've prolly already considered them, but w/o a doubt the single most pronounced gain stems from the humble and oft forgotten expansion chamber. While your "extended chopper muffler" and the mods you've done to it are awesome, the chamber is an integral part of a two stroke motor - left out only due to the low cost of the basic kit.
Porting your intake a wise move, it is as you've said it's only part of the procedure. Should you ever get an opportunity to pull yer bike off the road for a lil while, here's a very basic guide encompassing not only the intake and exhaust manifolds, but their perspective ports as well: http://motorbicycling.com/f13/basic-...olz-16646.html
Additionally, as we veered far off-topic as we are wont to do - there's pics of how to have a full length exhaust system that could include both your extended chopper muffler and an expansion chamber here ifn yer curious: http://motorbicycling.com/f13/cataly...ers-15857.html