Good morning. I need some advice. Sorry this is on the long side, I'm not familiar with Dodge engines.

I'm working on a friends 2010 Challenger R/T 5.7L Hemi. Around 75K miles. She had a radiator crack, overheated it, and as a result it had a bad head gasket.

I took the heads to a machine shop to check them, mill them flat, check valves, the whole 9 yards. So they were milled, valves and seats were re-cut, new seals and put back together.

I reinstalled with factory head gaskets.

Now, I reassembled and the clearances appear to be too tight at TDC for some cylinders. Some valves are open slightly and leaking during leakdown testing. After rotating the engine, I'm seeing bent intake pushrods.

So I suspect the geometry has changed, or I'm screwing something up during assembly.

My Questions:
if the pushrods aren't centered exactly in the lifter, would this cause this? I thought I had them in the lifter cups, but I suppose the loose ones could have moved while tightening the rocker support.
Do these stock springs bind that quickly if the clearance is too tight? Are the springs the same, intake and exhaust? I see some have paint on them. Possibly the machine shop didn't get them in the right places
I've ordered a pushrod measuring tool to check the lengths and see what size pushrods I may need order. Is there any valve lash clearance to use when measuring or just snug enough to not rotate the pushrod?
Could the timing have become messed up. Can the timing chain in these engines slip a tooth between the cam and crank if you crank backwards? I read there are issues with the tensioners.

Any help is greatly appreciated.
Paul