Would this be splitting it to replace the engine rear main seal..?? If so, did you get the clutch plate aligned..?? If so, sounds like your right there, all but going through the clutch disc, but just won't drop in the splines.
You can engage the PTO, and take either a 15" crescent/spanner wrench, or 1-1/4" open end wrench, and turn the PTO shaft to turn the transmission input shaft, to line up the splines. You can feel the spline alignment, through the wrench.
If you are that close, your bolts shoud be long enough to keep everything in line, so as to do some slight shaking, and pushing forward on both rear wheels.
Make sure you have an even gap at top and bottom of block and bell housing.