The 5 speed MUA tranmission is numbered MUA5-CT. That transmission was made by Isuzu and used in V-6 powered Isuzu Troopers from 1990 to 2002. So it should be relatively easy to find.
There was another 5 speed transmission which was also used in some V-6 Troopers from 1998-2002. It was made by Aisin, also has a 24 spline input shaft, and was numbered AR5. Since both of these transmissions were used with the same motor; I think there is a good chance that they are interchangeable. Aisin is known for the quality of its products; which are commonly used in Toyotas; and since that transmission was only used with the larger 3.5 liter V-6 (while the MUA was used with the earlier 2.8; 3.1; and 3.2 motors, as well with the 3.5); my sense is that the Aisin, which was introduced in 1998 along with the 3.5 motor, may be more durable than the older design Isuzu MUA transmission.
There might be some minor external differences between the two transmissions; but my sense is that they were made to be interchangeable.