I just rebuilt my engine and am having trouble with the performance once it warms up. Once the engine is warm, once you get around 1/4 throttle going through 1/2 throttle it pops and has no acceleration. Once you past half throttle then it opens up and has extreme power. Just to help with diagnosis if any of you have ideas the mods are: .040 overbore complete top end seals gaskets etc. dynajet stage 2 kit, k&n airfilter with lid off. Any suggestions please feel free to respond.  

it is possible that it has a timing issue, but it sounds more like it has a carburetion issue.

it sounds like it is starving for fuel even with the jet kit in low throttle.

try adjusting the fuel/air mixture screw out in 1/4 turns be sure to mark where it was setting before you started, and keep up with how many 1/4 turns you make.

if no change with the fuel mixture screw, try raising the needle by one groove, then readjust the fuel mixture screw.  

wolf1 sound like ya been around the block,i got 05 350 rancher smokes bad . looking to go 1mm over size(already got the piston kit),never been into these motors. can i just pull the head and cylinder,bore it out and slap it back togeather (no other inturnal work?) i know it will need to be retuned,but do i need to do valve adjustment?  trying to ride in two weeks???  

if you are using the old valves it will depend on the machine shop.

using the old valves make sure they don't cut new valve seats in the head. or you'll most likely have to revalve it to get them to seat all the way in.

but do inspect the old valves for wear.

if it is smoking it could be that just the rings are shot or it could also be that the valve stem seals are bad. or even both.

so do a thorough inspection of the valves and seals.

also it's normally a good idea to go ahead and install new seals everywhere.
extra compression in the cylinder means more pressure on the seals, and a weak seal will most likely start leaking.

1mm over is usually .40 over.
that's a decent hp and compression improvement.