Well It sounds like it's running too lean. Having to have the choke on to get it to barely run is setting up the exact opposite.
Too lean, hard to start, bog on acceleration, no power. You add the choke to somewhat compensate, by cutting off airflow.
Now you have an engine with little air and more fuel at idle. Open the throttle up and you dump more gas in it, with the choke on, so it starves for air and fouls the plug. Once fouled, I toss the plug. Too many times I've seen folks chase a problem all caused by a fouled plug.
I've seen fouled plugs spark like crazy when pulled from the engine. Yet when installed, the engine won't start, and the plug comes back out gas soaked like it wasn't firing.
If you increased the airflow via one of the bigger breathing air filters, and with a header that flows easier, then the fuel system needs to be adjusted to compensate. These motors tend to run on the lean side stock, and if the fuel system isn't up to the job making it flow more air is just going to make the problem worse.
One other thing. Load on the engine. Chain too tight, weak clutch springs, these put a load on the engine that shouldn't be there. Can cause the engine to start/run poorly at idle. So it won't run unless you richen up the mixture, by adding choke. Now you got a loaded up plug just to get the engine to idle. You give it throttle, dumping more fuel in an already over rich system, and the motor dies, as the plug fouls out.
My Predator ran like doo doo when I added a header and A/M airfilter. Like yours it wouldn't idle right, surged, and left alone would just die. Unless you had the choke part way on it would die if you tried to throttle up.
Installed a 36 Main jet, and new tube and it became a different beast. Now it will fire on the first crank, sit there and idle like a baby Harley, and crack the throttle and it's ready to rip the bike out from under you. More then enough for me, still has the governor on it.