Mew2Senshi: The Driver

My father and I are in the process of rebuilding a VQ35 out of a friend's Pathfinder. Apparently it blew a gasket due to overheating. The top end has been disassembled with the engine inside.

I would like to know about a few things before sending to machine shop and reassemble everything back. Would the holes from the back timing cover to the cylinder head be misaligned if the cylinder head were to be resurfaced in case of warping? Would a thicker gasket fix the problem? Speaking of gaskets, is it a good idea to replace all of them while I'm at it? Some look in better condition than others. Most important: are the head bolts torque-to-yield, or can they be reused?

If I'm missing anything here, I would like to know. Torque specs and sequence. Timing marks. Upgrades and what-not. Everything to make it last. I appreciate all the info I could get from you experts. This is the most complicated engine I've worked on to date.