So what did you use for rocker arms on this engine?? Non adjustable shoulder bolts?? Those won't work with anything other than the original stock heads and cam. Probably the cause of the valve train noise and why it wouldn't rev.
Also, look at the other pistons. Looks like a valve hit everyone. Timing chain installed improperly and was advanced or retarded too much and valves hit piston. BTW, been there and done that. I bent 8 intake valves and broke a bunch of rockers.

The heads are stock L29 heads on an L29 block. The only change from stock was the mag cam which wasn't enough of a difference to do much of anything and a Summit timing set. Valves, rockers etc were stock.
The timing set was setup at zero and installed correctly, but I'm wondering if there was a problem with it. I couldn't degree the cam correctly for the life of me. I didn't have a cam card so I just went with it because it was a stock cam. Never had that problem before and I should have stopped right there I'm sure.
The valve train noise was the intake lifters just barely kissing the pistons for sure. I checked my notes and I had plenty of ptv clearance. Intake .102" Exhaust .168".

How did you check ptv? To go from .102 to less than 0 something changed

Light spring, TDC and a dial set up on the retainer. You have a good point and the only thing I can think of are push rods or rocker arms being wrong. God knows it wasn't the . 484 lift cam...

I don't believe using the wrong push rods or rockers are going to change the PTV clearance. They should at the very least be consistent. Compressed lifter while taking the measurement will change it, but 0.102" with a light measuring spring is quite a bit. IMO

What was the lift on the stock cam??

Why would you think pushrods or rockers wouldn't change the PTV clearance? Effectively more lift is going to push the valve down further towards the piston. What if the rockers were 1.8 instead of 1.7 or the pushrods were too long?
The stock cam is .480/.483 and the mag cam is .483/.483.

My thoughts too

How did you measure piston to valve clearance? By the questions you’re asking I’m pretty sure you did it wrong.
I put clay on top of the piston, torque the head down, assemble the valve train for that cylinder, rotate the crank 2 revolutions, pull the head off, measure the compressed thickness of the clay.
so unless you checked it with one set of pushrods and rockers, then ran the engine with different parts you’re piston to valve clearance didn’t change

Even more basic question, was the block milled and/or the heads decked and the actual measurements of clearance not accounted for as the components were "stock"?

Just throwing that out there as the pics are showing more than one piston contact.