I know I'm late to the party here, and it's been awhile since I've posted but im going to add my .02 to this discussion. For starters, you do have an alignment issue, that's a fact, as it's been discussed here, aftermarket heads change the geometry and location of the intake and exhaust ports in a lot of cases. The problem you are seeing with the misalignment of the rocker arms is a simple fix, and pretty much all manufacturers make a set of offset guideplates to combat the very problem that you are seeing to correct that issue. It's a simple thing of what heads you have generally have a recommended/required parts list to go with them, most of the offset guideplates come in I believe a .150" offset to straighten up the rocker arm side to side geometry. You can run self aligning rocker arms, or install the correct guideplates, you can't run both, However, I have issue with the pushrods as well. A couple of things to take into account here. I know it's been said that the "contact" patch has been checked, but if it was checked with anything but a solid lifter, I can assure you just by looking at your pictures that the pushrods are most certainly the incorrect length for your application. Once you go adding aftermarket heads with a generally thicker deck/flange surface and most aftermarket heads run longer stemmed valves, and then you start decking the block and adding different thickness head gaskets and installing a roller cam and lifters suddenly the original valve train "geometry" is out of whack. I've seen cases where we've had to install pushrods as long as +1.100 to correct geometry issues on engines. Installing a roller camshaft and roller lifters generally can change the length of the pushrods sometimes by as much as a couple hundred thousands of an inch at a minimum, and then add back in thicker aftermarket heads, taller than stock valves, etc. it NEEDS to be checked and verified. And if it's being done with a hydraulic lifter in place of a solid lifter, you will NOT get a correct reading nor make a proper determination of push rod length. Throwing in +.100 length pushrods just because is asking for problems. I'm not saying you're going to have catastrophic failure, but you're valve train will be unstable at the very least. There are many variables involved and sometimes putting the correct parts in solves many other issues as well. For example, the rocker arms kissing the valve covers, even though those scorpions are a larger than most body. And when it comes to rocker arms, and valve tips, you generally want the rocker arm roller to "start" somewhat on the inboard third of the valve, and roll across the center of the valve stem as the lobe pushes the valve stem down (open) and end up somewhere on the outer third of the valve stem at max lift. Understand, that this is somewhat of a cliff notes version of checking geomtry, but getting it right now will keep you from having headaches in the future. I know I'm getting slightly off track here, but everything discussed in this thread needs to be checked. I'd be more concerned with proper geometry than I would the studs being .025 or so "out of round" although I agree that seems like quite excessive run out. Get em "squared" up first and then worry about the other stuff.
