Sorry if I'm bringing this back but I wanted to throw my 2 cents in too.
I did this swap with me and a friend and a manual and yeah, it took us two days (though we didnt work that fast).
Regarding the clutch and pressure plate, you CAN do this without the alignment tool, it just makes it harder. It was a bitch for me and my friend as the actual swap was a tranny swap and thus an old flywheel and used clutch didn't wanna hold too well. What you do is get a screwdriver in there when you tighten the pressure plate bolts, and sort of imagine where the clutch is to be centered. Then when you put the tranny on and start torquing the bolts, the mainshaft of the tranny will align the clutch. If I could do this again, I'd rent or borrow one, I heard there are plastic ones at autozone or somethin for like 5 bucks.