Does yours have the three-speed or the four-speed? 88+ got a four-speed, which is easily replaced with the later four-speeds (including the one from the first-gen Xterra). If you've got the three-speed, you may have a bit of a project on your hands converting the wiring and computer to run the four-speed, and sourcing parts to rebuild the three-speed might be a whole other challenge. If you want to go manual, the '96+ transmissions are slightly revised to hold up better, so you might as well take advantage of that. (Earlier boxes tended to have issues with the countershaft bearings; later boxes moved the fill hole up slightly to increase the oil level.) Any Pathfinder, Frontier, or Xterra with the 3.3 should have the updated trans. Takes a little screwing around to do an auto/manual swap (though there's at least one good thread on here from someone who's done it), but the good news is the engine computer won't notice or care.