General update:
Today I went back home to work on the wagon. I replaced the fuel pressure regulator, ECU (516 to 935), rear airbox cover (old was cracked), and did some hose-patching.
One of the small hoses that connects to a nipple before the throttle body had cracked, so I cut it and put it back on. I need to figure out what it does and it's origin so I can replace it at the source. It's cracked several times over the years.. I also noticed that the flame trap hose had a crack in it where it fits over the flame trap, so I coated all of that in a ton of RTV and ordered a replacement. I don't like to RTV stuff but it might help track the issue if it's air leak related.
My dad and I think the car actually runs smoother then before, with him saying it's the best he's ever seen it run. The problem with this is I put in engine mounts a while ago so that may be what we're seeing. I haven't driven the car yet since I'm still afraid of it dying, but also haven't had time. The hesitation issue is what really bothers me.