Always separate the trans from the transfer case. The transfer case adds a lot of off balance weight which can make it near impossible to line up the input ans the bell housing at the same time due to the transfer case trying to twist the transmission off the jack to one side.
97 F-350 XLT CC DRW 4X4 PSD, 285/75-16 Custom bumpers, Gauges-boost/egt/trans, Swamps IDM, 3.5"dp- 4" exh., 3" Body lift, ES bushings/mounts, Built trans, billet conv, B&M pan, Hayden cooler, Adrenaline, stage 2's, IC, H2E, E-fuel
ARP's, 910's, Smith Bros. to come
No real tricks.. I usually just put the transmission in gear(any gear) and if the input splines aren't lining up just right, reach back and spin the output shaft a bit so the input splines will line up. Pulling the shifter stub will help with clearance, but I've never had a problem with it being in the way too much.
I would pull the transfer case also. That's easy to put in once the transmission is in and only makes it more of a PITA to get the trans lined up right.