In my opinion, going from the CR CDI ignition to a breaker-points ignition would be a huge step backward. The CDI's electronic advance adds a ton of low end, in addition to all the other benefits of CDI. I just readjusted my MR's CDI for more advance, and was amazed at the extra low end and midrange power I picked up.
Perhaps Ricky Stator can add a lighting coil to your CR ignition, but if all you want to do is pass a DMV inspection (if any), I would strongly recommend battery/LED lighting, maybe using MR250 or XR lighting hardware/switches. Check your DMV regs; in CT they want to see an odometer.
I've been using 2-stroke engine development software (EngMod2t) for a while now, and if you want to make your pipe work better at lower rpms, add some length to the center section of the pipe. This maintains the cone tapers and header/diffuser tuning, but delays the return pulse for better cylinder filling down low. Lenghtening the diffuser with a short md-cone extension will help even more, but may reduce overrev power a bit.
And don't forget gearing, although with the close-ratio CR transmission your top speed may be somewhat limited (my CR125 topped out at 52mph with stock gearing).
Clarke Mfg. (
http://www.clarkemfg.com) may make an oversize tank to fit your bike.
Ray