Engine and Trans removal together?

Why will the car need an alignmentif it is aligned properly to begin with? Can you be specific?
Never having removed from the bottom, I might have stepped in it on the alignment issue. It depends on what you remove. I was thinking most people unbolt the upper control arms, in which case it would need a front-end alignment. If you disconnect the upper ball joint (has come out easy for me), you should maintain alignment. If you disconnect the lower ball joint (much harder) as one suggested (and MR4V's photos), you are leaving the spindle with the body so need to also disconnect the tie rods, though that should still maintain alignment. BTW, the $7 1000 lb wood dollies at Harbor Freight work great.

Re lifting the body, I like to support it from the the frame rails with a lattice of 4x4 lumber. I have old fence posts I cut into shorter pieces. I feel a lot better crawling under the car like that, compared with supporting the frame on just jack stands that start looking skinny with the whole car floating on them. I also have a few jack stands under just in case, and I slide the wheels under the frame and put wood on top as a final support to give enough space to breath. We do get earthquakes here. I just keep adding rows of 4x4 as I jack it up further. Best to start by backing the rear onto ramps or jack and support the frame there first.