I've never needed to use alignment rods myself but I think those who do install them before muscling the trans around, not once you are sliding it home. At the home shop, I use a floor jack with an attachment. I like to get it started through the T.O. bearing then I push and wiggle it the rest of the way in. At work I cheat and use a hoist and tranny jack. I've also heard tale of using a cherry picker through the floor when R&R'ing 4 speeds.
To each their own,
Scott
