Look into changing the expansion chamber (tuned pipe).. there is a MASSIVE amount of math required to design them properly, but they are the key to 2 stroke power. I think EFI might be hard to implement since O2 sensors will get all confused by the scavenge air, so closed loop and feedback of any sort is out... You would probably be looking at an Alpha-N mode instead of speed density.. so you'd base your fueling solely on TPS and RPM, not on manifold absolute pressure (MAP) and RPM. Megasquirt is probably the ECU to look into, I think it's the most customizable, at least from a DIY standpoint.
About expansion chambers, TANSTAAFL.. there ain't no such thing as a free lunch... I don't know what kind of power band you have currently, but you can tune the chamber for a nice wide band, of if you have close enough gears, a violent boost of power over a narrow RPM range.
I have been playing with 2 stroke tuning for a bit.. Since they're cheap, I do it with chainsaws.. Here is a bored, stroked, ported and piped Husky 61 (48x34mm is now 52x36mm bore/stroke) now at 77cc... I designed the pipe, and I could get more out of it with more aggressive exhaust port timing, but I want it to be usable without the pipe too... Originally the saw had about 3.5hp, it's probably around 8hp now... Peak power is around 11,500 RPM, peak torque at about 10,500RPM. That is a 34" bar (They usually had 20" bars)
It's a lot of fun, just be prepared to need new pistons and cylinders.. when you start pushing really hard you've got to count on blowing some up.Oh, and keep the sticky side down!