Sometimes the cel comes on for a 4/second period every time you start the engine.
This is the fuel priming the injection system, wait till the light goes off before starting..
Your idle may need to be bumped up 50/rpms so it doesn't stall. the jardine muffler opened up the exhaust so a better idle may be all needed to keep it from happening(Stalling) that is .
Possibly the Throttle position sensor needs to be looked at.
Run some Seafoam in your fuell tank to clean out the injectors, just follow the instructions for adding NOT the Whole Can at one time.
Hopefully the bike just needs to be Tweeked a bit.The Jardine is hard to tune so try the small inexpensive things first, hope it is an easy fix. *Jimi