Norm,
You didn't specify any steps you had taken to assemble the top end (checks to insure the cam was properly aligned prior to buttoning up the engine). Do you have doubts that you may have incorrectly set the cam timing?
Prior to taking the drastic step of removing the engine, I would attempt to double check the valve timing externally.
First, disconnect the battery (safety step). Remove spark plugs 1 & 4. Remove the points cover (OK, not sure if yours has points, but the lower engine timing cover) on the right (throttle side) of the bike. Using a suitable wrench, rotate the crank to the 'T' mark for cylinders 1 & 4 (also top dead center - TDC). You can physically verify this by placing a long screwdriver into the sparkplug hole until it contacts the piston top. CAUTION!!! Make sure it won't fall into the spark plug hole!!! While holding the screwdriver lightly against the piston top, rotate the crank just a few degrees in either direction and note that the piston tops out at the associated 'T' mark. Once confirmed, remove the valve adjustment caps for cyls 1 & 4 (don't forget to take out that screwdriver in the sparkplug hole!) At TDC, either the #1 or #4 cyl should show both valves at maximum clearance (should be able to wiggle both the intake and exhaust tappets). If this is correct for either cylinder, rotate the crank 360 degrees (this rotates the cam 180 degrees) to the 'T' mark again and now the other cylinder should have the loose tappets. If this is also correct, I would first recheck the valve clearance for all four cylinders, and recheck the cam chain adjuster. No reason at this point to pull the engine if all this is correct.
If the tappets do not wiggle at the expected degree of rotation, you can try to advance the crank and see if the condition exists at another degree point. If you find either valve tappet pairs become loose at another point, try to go another 360 degrees on the crank from that other point to see if the same is true for the opposite cylinder. If you discover that is the case, then yes, the cam timing is incorrect and sadly, yes the engine will have to come out to correct....
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