When you put your top end back together, did you 1) back out all your tappets and tie the rockers up out of the way before reinstalling the valve cover, and 2) set your valve clearances before just firing the motor up?
When I did my top-end, I accidentally installed the cam 90 degrees out, like Scottly said, by using the T23 mark instead of the T14 mark. Luckily, I was able to catch this early because I tried to set the valve clearances and could not get them right. After some mental re-calculations, I decided to pull off the valve cover and discovered the problem and fixed it.
The reason I asked about backing out the tappets is because you risk bending your valves if you reinstall the cover and just crank it down without making sure the tappets aren't catching on the valve stems unevenly (at least that's what I think does the damage...).
Bent valve stems might cause the problems you described, but it does sound like your cam timing is off. One is an easy fix, the other is not...