Did you use the rubber band trick to make sure all of the followers were up and out of the way when you reinstalled the cam cover? You don't actually *have* to use rubber bands, but the important point is that none of the followers bind against the tips of the valve stems while the cover is being secured, or they can become trapped and damaged. Look through each of the eight valve adjusting holes to make sure, if any are out of position, remove the cover and carefully inspect for damage.
The camshaft being out of time with the crankshaft would make the most sense, and if it is then there should be a spot somewhere in the rotation of the engine where both valves are loose. If so, this may confirm that the timing is off. If not, then something else is not right. You mentioned 'rebuild' but did not elaborate, any chance the cylinder head received an aggressive valve job, and the valves are now seated too deep in the head, eliminating the normal space utilized to set the valve clearances? This is not a common occurrence, but it is possible.