I had similar issues. Turned out to be the battery as well. But check all your connections and make sure there are no drains on the battery.

 

i also have this problem i bought a new starter clutch and a new battery and it still does it. the bike shop where i live cannot explain why it does this neither can the other shops i took it to. so im getting a yfz to get rid of the hassle and putting that kick starter on it to help eliminate the electrical issues.

 

I just had overhauled a Raptor as well for a customer, I installed a 686 kit with a Wiseco high compression piston and a stage II cam kit with springs and all of the good stuff. As well as a dual exhaust system, freaking awsome ride.. But it was very hard to start do to the compression in the engine, I replaced the battery and it was way better. But after some ride to break in the engine. It started up easier and easier as time went by. The head was also heavy modified with port and polished etc. Good luck,, Rich