I've been trying to sort this out. Bike starts and idles fine. As soon as I open the throttle, it pops/ backfires through the carb.

-No vacuum leaks- checked w/ starting spray while running
-New boot
-Carb is clean and original
-Timing is on the mark
-Timing chain is tight- no play
-Valves are adjusted to factory specs
-Cam has clean lobes

The original CDI burnt out, and I replaced it with a factory CDI (those aftermarkets did not work.. so, $300 later...).

IF the neutral switch/ sensor has failed, would it cause the CDI to go into "limp" mode? As the neutral light on the dash doesn't light up when in neutral. Plus, I cannot start the bike in neutral... It almost seems like it's running in a "limp" mode, where it's cutting out spark (although when it pops out the carb, fuel is spraying out of the carb).

Interestingly, every now and again, I can catch it where I can get it to rev to a high RPM without popping for a few seconds.. then it begins popping again..

I am stumped. I took it to 2 shops and they have failed to figure out what it is...

 

Check the voltage at the battery with engine running, if it goes over 15v it may be cooking your CDI. Always do this after fitting a new CDI and, before fitting one, check all wires to the CDI are working correctly, particularly earths. There is obviously a problem with the ridiculously over complicated neutral "lock-out" system, fix it. The poor running could be a blocked exhaust, try it without the silencer.