Dropping engine back into my E body,auto trans in place...any tips on mating the engine/trans?

Line up the dowel pins if you can, if not, just get the mounts to drop in correct location, then get under car with a prybar or two to line it all up. You shouldn't have to struggle with it too much.

Just make sure that the torque convertor is all the way engaged to the transmission and the nose of the convertor is lubed in the seal area. The FSM is kind of vague about it and specifies a Miller Tool to align the shafts. There are three alignment points, the notch in the torque convertor nose and pump and the two shafts. With fiddling, they will all align and the convertor will go all the way in. When they are mated, the convertor should be about 1/4 to 1/2 inch behind the flex plate. If they are not, then the convertor is not engaged right. Torquing the bolts into the convertor will draw it back out to where it belongs.
Also, make sure the two dowels are in the transmission.
Oil filter on the engine has to be off to put the bolt on that side in.
Thats about it.
Craig

Thank you.