When looking for a used transfercase, be sure to check a few things. If you can lock the input and rear output flanges, the front output should have a ton of resistance, but still turn very slowly(not a sure test, but gets you started). If you can easily turn the front output by hand, its a sure sign the VC is bad.
Grab the front output and wiggle cw/ccw to feel for a clunk-clunk. A very small amount is normal, but a heavy sounding thunk is a chain that has stretched. Most chains will stretch over time, but the tighter the better.
Look at the front output flange splines, they should be straight cut, with no rounded teeth or a step part way along their length. This flange can be replaced, but I've never done one and don't know where you would find one.
The chain, VC and output flange in your auto case are all the same as in the 5spd. So if yours is good and you find something wrong with your new one, you may have to get a little more in-depth(a lot) but all is not lost.
And yes, when you put a new shaft in, use spacers so you can be sure to get the best spline engagement. There is a lot of talk on this topic on e30tech.com's ix section.
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