For the engine mounts, I would suggest:
- remove the header
- unbolt the engine mounts from the frame on both sides
- use a floor jack and a piece of wood to lift one side of the engine from the block
- replace the engine mount on that side
- repeat for the other side
This would also overlap with the overpipe installation as you should move the overpipe into position while you're replacing the mounts on the passenger side. I would feel very uneasy about trying to jack the whole engine up to replace the both mounts at the same time because you would essentially be balancing the entire engine on one small jack point. In my opinion, it's much safer to do one side at a time and doing it that way should alleviate some of your concerns.
As you've already alluded to, the hardest and most time-consuming part of this installation is going to be breaking the old salted nuts (lol) off. Some angled/joint sockets might help there as well. Also, loosely thread on all of the nuts for every connection and get everything loosely connected together before torquing them all down. Be sure to get back under there after a few heat cycles to check the torque on the nuts.
We've had our cars for about the same amount of time and I'm glad to see you finally starting on power mods. I'll probably hit you up for some switches soon!