I just had to pull the head off my trx 300 fourtrax to redrill and tap for one of the studs on the exhaust header. Since I did that and threw it all back together, I realized it was time for a new head gasket (thought I could get away without one) as there was pressure in the crank case. And since then the timming chain was clicking. So its torn down for the second time ever in the last 14 years for a new timing chain and head gasket right now.
Back on topic, I noticed last time I disassembled, and reassembled the top end that the hash marks on the cam were a little off when the engine was at tdc whether I moved it forward or backward a link. I think that might have been due to a streched timing chain.
Make sure its at TDC according to the flywheel, no matter what. Then line up the cam hash marks flush with the head as close as you can. If anything line it up so that when your looking at the hash marks the cams tilted a little bit towards the back of the quad. Then put in the cam chain tentioner which should take up the slack in the chain and in result line it up for you.
03 LTZ400
-Full pro curcuit exhaust
-Intake
-T9 Baja beadlock rims w/ holeshots
-Extended DuraBlue axle