We'd have no idea how a flywheel, that's "hard-mounted" to the engine can cause any kind of glitching...unless the receiver antenna's either been cut down or is improperly-routed and too close to the engine. You need to check your R/C equipment. Glitching isn't caused by the engine, other than the vibrations shaking something loose. You may also wish to consider a failsafe.

The stock pipe is fine, and will help the bottom end a bit.