PROBLEM RESOLVED
After some careful analysis, I noticed the idle adjustment screw had been laying on one of the fins, this caused it to become metal to metal. This also cause an abrasion to the front spark plug wire. I check with some mechanic friend and they told me it was causing arcing in the intake.
After this was found I noticed the bolt that held the manifold to the coil bracket had fallen out. This caused the manifold to wiggle a little causing intermittent leaks in the intake manifold.
Just to be on the safe side, I changed them out with some new Genuine James JGI-26995-97-X intake gaskets. I swapped them out, and make sure everything was nice and snug.
I also changed out the fuel sock filter, inline fuel filter, O2 sensor, cleaned the fuel rail, and cleaned the injectors.
After a closer look, I ended up changing the timing maps, and re-tuning the fuel maps from scratch. About 15 hours of data logging, and quick rides, she is starting up nice and and the idle is clean at 995 rpms.
MODS:
KnN air filter
Open Air BOX
Breather re-route
Jardine GP-1 exhaust
If anyone is having any issues with their fuel maps give me a shout, I can send you a copy of my ECM and you can try out the maps. It might not be 100% but atleast it will get you close, if you have the same setup as I do.