I just had the 4 speed out and back in without using alignment pins, mostly because I didn't have any, and because I did have a proper transmission jack. The screw drive scissor type with a ratchet strap to hold the trans in place, and a bit of 2x4 on the passenger sump area to keep the trans from rotating. I've used the same tooling in the past to swap other transmissions and this was actually pretty easy considering aligning the input into the clutch disc is all visible and not hidden by the bellhousing.
If I was using a cherry picker, floor jack, or 4x4 through the door then alignment pins would be a whole lot more useful. I'm just providing an alternate solution to a common problem.
