What kind of Jeep? If it is a Cherokee or a Comanche, they used the Peugeot BA10/5 gearbox in that year, and it's a piece of shit to begin with. I have one that - by some miracle - has survived 213K miles to date. I am looking for an NV3550 or 4500 to build up and bolt in its place sometime soon...
As far a "brand new" transmissions, they CAN be had. They are also very expensive, as they come from places like Advance Adapters and Drivetrain.com. A proper reman will use a measured good case and maybe shafts, and Magnaflux everything else, replacing as necessary. This is also how I approach my own rebuilds - I am usually on better terms with a local Machine Shop than I am with a repair shop (most garages don't have Magnaflux gear, and some of the other nifty stuff I like to have access to...)
For the BA10/5, the NV3550 os nearly an effortless swap, and the 3550 can be found in most pull yards under CJ/TJ/YJ, and parts for rebuild and reconditioning are readily available. The NV3550 is the same length as the BA10/5, and the shift tower is only "mislocated" by about 3/4."
If it is a Cherokee (XJ) or Comanche (MJ,) feel free to visit us at www.naxja.org and we can probably teach you how to rebuild the thing yourself. Good thing is, most manual transmissions are quite simple...
FFZ
87XJ, 88XJ, 89XJ, ...