Sounds like a great motor that you've obviously taken your time on.
Like you, I believe that one of the main limits of the motor is the head. Tim at DOA does a great job porting these heads and will provide you with flow data after porting. Ted (engnbldr) also has a son that does this work, but I've never seen it first hand.
It's pretty easy to clean up the intake ports on a 22RE, but I leave the bowl porting to the experts.
These things are designed for low end torque, so it's hard to completely kill the results of a really long stroke.
My understanding is that with .5mm valves there isn't much of a downside. At 1mm, you may lose torque - and again - this is the desktop dyno talking, but we're talking about a slight loss in a range where you're not producing a lot of power anyway. Using Engnbldr's stuff, I've never had anything but improvement over the whole RPM range, but that that's against a well used motor.
Blowers.. I don't like the blower design or results from using the Camden (LCEngineering) supercharger on the 22R... It's simply too inefficient. Never run it on the 22RE. It'd be great on a trail truck where you don't have mileage concerns, but I don't like it much for street use.
