Hmmm, I would seriously consider triple checking that cam timing.
If its off a tooth, it will still run, but you'll never get the jetting right.
On this engine, a tall-tale sign of cam timing being off is having to go richer and richer on the main to try and get it to run.
I cant remember for sure on this engine, but I think the timing chain can be off 1 tooth (half a tooth) off every other 360* to TDC. I've seen this on several Yamaha and Suzuki engines before, my old GSX-R and Bandit are exactly like that.
On some engines, for example - If you line up the TDC mark at the end of the crank, the chain and cam timing mark arent exactly lined up, VERY close though, theyre just slightly off (the infamous half-a-tooth mistake). Pull the cam, and rotate the crank one turn back to the TDC mark on the crank again, and the chain and cam timing mark are perfectly lined up.
I've seen this quite a few times - guys swear the cam timing is OK, only to find out it was off a tooth when it wouldnt jet worth ****. Hell, I've done that myself before on an engine I've torn apart a dozen times.