Glenn - if you haven't already done so, check the axial movement of the input shaft before pulling it out to replace the needle bearings on the end of the mainshaft that were mentioned earlier. If you have more than the . 006" of play, you will at a minimum need to check the 5th gear nut on the output side of the transmission. Don't know if you have the upgraded mainshaft or not, but either way, you will need to check it out. If the nut is still tight, but the end play is excessive, then the bearings are worn, and you will have to make a call if you want to risk it and shim the bearings or just rebuild the transmission.
Remember to purchase new bolts for the flywheel and input shaft bearing housing, replace the rear main seal if it is leaking at all or has a lot of miles, and check the aluminum tailshaft housing (5th gear cover) for any cracks.
Suggestion on the jack - I use an ATV jack also. Purchase a pack of door installation shims at a home improvement store to shim under the transmission to get the angle correct for going back in. I raise the rear axle up on jackstands so that the transmission is level, or fairly close, to make it easier to get the alignment correct.
Thanks,
Jeff