Hi,
The fact that the bike is starting is a good sign, it is a good indication that the ignition system is probably ok. What you are describing is still fuel related in my opinion, now that you are getting fuel to the engine it may actually be flooding. Removing jets and the like is ok if you are certain they've gone back exactly right, it is possible to overfuel an engine very easily with an incorrect jet setting.
First thing you should do is start the engine, then without letting the revs drop, adjust the the idle screw. This video is pretty good, the guy seems to have a good grasp on why he's adjusting unlike some of the videos.
Cheers
http://www.youtube.com/watch?v=A1vRMERs4RQ&list=PLaJTfkzrS4lkxKrukbFidxIZ0H0KZnl0i
westcountry, December 2013