I just went through this and had the same problem. Turns out that I needed to bleed, bleed and bleed again to get my brakes to come back. There was air in behind fluid. The driver side rear would pump fluid... then on about the 3rd time trying to bleed it it blew air out.

I didn't have any trouble getting axle shafts back all the way in.Once the splines were lined up I was golden.

Good luck, let us know what you find.

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33" AT Winston Wheelers. Nearly New.
all stock except for 4.88s...