It might be that you haven't yet adjusted the tappets? The clearance for the intake valves is 0.002"-0.003" and the exhaust valves are 0.003"-0.004".
If you dig into the (Honda) manual it will show you a table that indicates that you set the crankshaft at the 1-4 "T" mark and then adjust the little adjusters for either cylinder #1 or #4, whichever happens to be at overlap stroke at the time, along with the intake or exhaust for cylinders #2 and #3, and the opposite ones for #2 and #3 after turning the crank 360 degrees again and adjusting whichever of #1 or #4 wasn't adjusted the last time around.
It isn't necessary to have the tappets adjusted before setting the cam chain, but some manuals seem to think it must be done in that order. It does help, though, when trying to discover whether the cam is at the correct position for setting the cam chain. Usually it should be set just as the #4 intake valve is starting to open at about 15 degrees past TDC for the 1-4 timing mark.