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I've never done what you are doing, but I have pulled my transmission several times. When you separate the transmission/transfer from the engine they tend to tilt a bit. You may have to put a jack under the front or rear of the transmission/transfer case to get it back to the correct angle for the install. Simillary, you may need to tilt the engine. The transmission input shaft needs to be along the same angle that the crank is.
Did you use a clutch alignment tool to line up the friction disc in the clutch? Did you remember to remove the tool? Is the clutch still alligned.
Finally, you may need to rotate the input shaft to get the splines to line up with those on the friction disc.
When it's close enough, if you can get one of the bots through, you can start to tighten that (but don't force it!) to pull the two together.
Good luck.
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