The gear ratios are practically the same in samurai and trackick trannys....so no real benefit to swapping it for that reason.
If it is a 4wd tranny, you could put the tracker tranny and tcase in and do a "kicker 3" setup. Note, that there are a lot of mods to the tcase and tranny tunnel that would have to be done, to do this.
Or you could remove the tcase from the tracker tranny and install the tranny that way (still have to do tunnel mods, as well as intermediate shaft mods).
If it is a 2wd tranny, you could install it. But again, you would have to mod the tranny tunnel and intermediate shaft.
There really isn't any benefit for you to use the tracker tranny....unless you are needing lower gearing (by using both the tracker tcase and the samurai tcase).