I have a 1990 Tracker 4X4 automatic and a 1990 Sidekick 4X2 manual. Is it possible and how much trouble would it be to put the manual in the 4X4 and the auto in the 4X2?
TIA

You can't convert a manual 4wd transmission to 2wd, because 2wd has a longer tail shaft (unless you tear transmission apart and change it).  It would be a guess that it is the same for automatics.
You could convert the 2wd manual to 4wd by adding the missing pieces.  The tail shaft on the transmission could be cut down so the transfer case can bolt up to transmission, or get the Transmission & Transfer already bolted together (or tear apart and change shaft, after you find one).
Converting both of them is twice as hard as converting one 

Y would u want to make the 4x4 less capable off road