One trick I learned for spline alignment is to put the transmission in a high gear, transfer case in 2Hi, and spin the transfer case yoke as the splines are trying to mate. It just won't get in and suddenly it will pop and slide right in.
Can you manually turn on the starter? On most starters there are 3 pins. The little one triggers the contactor to engage the starter. If you can jump 12 volts from the positive terminal over to it, it should turn over regardless of whatever else is going on.
Just make sure your...
One of the advantages of the YJ tub is that the rear inner fenders are squared off. Makes it much easier to build storage and racks around those fenders than the rounded TJ fenders. The frame is 1/8" thick, so it shouldn't be terrible to work with
Will it come out on an intermediate position? Try at every possible position of the key. Pull the starter relay or fuse if applicable to test the starting position.