Did you remove the u-joint ball cover from the torque tube as well? That would get you another inch or two. The Service manual doesn't mention that, but does say to use a jack to raise the torque tube.
The cab may be sagged a bit on the rear shackles, giving you less room. Maybe blocking the rear of the cab up a bit would give you enough room to remove the tranny.
[on edit] The frame is tapered (wider at the rear) at the transmission support crossmember, so it shouldn't be that hard to get out if you push it toward the rear of the truck.
Also, there's no gasket between the tranny and bell housing, so unless you're opening up the tranny (as recommended by others -and also me) all you would need is the u-joint bell gasket kit. That needs to be reinstalled off the torque tube so you can select how many gaskets you need between it and the tranny. Check the shop manual for the procedure.
