It will work but, as you mentioned, there are connector issues. I will look for some threads on the subject. The old trans uses a vehicle speed sensor (VSS) for the speedo/odo and an output shaft sensor (OSS). The new trans just uses an OSS for everything.
Expect to have the VSS/OSS issue to contend with. The output signal of an OSS is NOT compatible with each other.
IMO, you should at least talk to a transmission shop to see if the tail shaft VSS from your old transmission can be transplanted to the new. Also, remember to keep the harness from the 96 as the harness is different.
While you are at it, be sure to keep the DTR from the old transmission as well.
I am sure that you have at least looked at the cost of having your old transmission overhauled. Look for a shop that will take "bench" jobs. At the end of the day, the extra cost of a bench job over haul will get you a "zero" mile transmission that is set up correctly may be a better deal than an unknown salvage unit plus the hassle of the VSS.