The block of a 1HD-T & 1HD-FT are AFAIK the same (the 1 tells you the bottom end revision, the HD tells you the bottom end 'family', the T and FT describe the top end) so even if you're mixing 12 & 24 valve I doubt that will cause problems. The A440, A442F auto box's and the manual all bolt up the same AFAIK. The only thing I'm not sure about is if the flywheels are different between manual and auto to account for clutch v torque converter mounting.
The only tip I can think of is for getting at the top bell housing to block bolts. You'll need to remove the centre console and gear selector linkages, un-bolt the gearbox cross member and lower the gear box as far as you can, then with a pair of long drive extensions you can get at the top bolts through the selector hole in the transmission tunnel. If the gearbox is staying in then bolt the cross member back up before engine removal :D
If you don't have an FSM look on ih8mud for links to them.