I realize that this probably does not qualify as "hard core", but it is already in the "non-hard core" section, and it's a little slow over there. So...

I'm swapping an AMC 360 & Ford T18A in place of the 258/T5, in an 85 CJ7. I installed the V8 frame horns and have the engine & tranny installed. I'm pretty sure that the drive-train should be pointing straight back, in a perfect line, to the rear of the Jeep, unless there is an offset somewhere between the crankshaft and the output shaft of the tranny. It is pointing straight now, but the motor mounts and frame horns are not in the exact same position on both sides. The passenger side is twisted a little to the rear. Should I concern myself with this misalignment, or just be happy everything else is correct and torque the engine mounting points down, including mounting the tranny to the skid plate?

You should be good to go.

tighten it down

Some manufactures (Dodge and Ford) offset their engine to the bay, so that the driveline is not straight. GM raises the tail shaft. They do this to work the u joint and keep it from drying it up (or wearing out) in one spot and then burning up. That's what it sounds like to me that you have going on here? If so, no worries...