Yes, the waterjet is a sweet rig all right!
The valve seats should all be of a uniform height if you've had a valve job done. Then whoever assembled the heads ideally should have used a height mic and the necessary shims to set all of the spring heights to whatever number called out by the spring company. If all of this was done, then you shouldn't see any valve tips lower or higher than the rest. Remove one of the rocker assemblies and put a straight edge across all of the intakes and then exhausts and see if you can see any daylight under the straight edge. If not, then you might try my idea of measuring the pushrod deflection with the rocker assembly loose, then tight. If you see more than say .070" between tight and loose, then I'd say your machine work has resulted in moving the rocker rails too close to the block deck. Your pushrods May be too long. You might need shims like me. I have some extras, but we need to know if this is really what's going on.
Then again, the opposite might be true. With the rocker rails cinched down, can you move any of the pushrods? The pumped up lifters should allow them to spin, but not migrate up and down at all. Of course, some of those rods will be pushing valves, so they should be nice and tight anyway. Rotate the motor by hand and see if any are noticeably loose.
There's a lot of variables going on here. Because you don't know the exact history of this engine, it really needs to be logically diagnosed one thing at a time. If you don't find anything wrong by doing the above, then it makes sense to put a dial indicator down each lifter bore and see the height of each cam lobe as a helper rotates the crank through the nose of each lobe. This is a pain, but like checking everything else I suggested, its a solid diagnosis, not a guess.
And if you want to set your mind at ease, buy one of those oil filter cutters. They'll allow you to pop the cover off your filter and examine the element for trash. Cams and lifters are magnetic, so if a lobe is trashed, you'll see specs sticking to a small magnet as you drag it through the folds. If it comes up clean, you'll know you're still okay.
Keep in touch!