Is the tranny in gen 1s different than gen 2s? I was told that the wiring in the tranny is different.

They all use the 4R70W.

The '98 transmission has a stronger part that makes it less failure prone than the Gen1's and the '97 model.

As far as wiring goes, there is an actual wiring harness in the earlier transmissions which connects each of the solenoids and the TOT sensor in the transmission.

The later transmissions have a printed circuit board instead of the wiring harness. That PCB has its bulkhead connector pin-outs arranged in a different pattern than that of the wiring harness used on the earlier transmissions.

so what would I have to do to put a newer type tranny in my 93?

Mandatory:
Swap the following electronic components from the '93 transmission to the new one:

MLPS
TCC Solenoid

...and do one of the following:
1. Re-arrange the pins on your bulkhead harness (the main electrical plug for the transmission) so they match the new transmission's PCB.

2. Remove the PCB, and swap the wiring harness from your '93 transmission into the new one.

If you're swapping in a 2000-2002 Mustang transmission, you'll also need to buy either a speedometer gear with 20 teeth, or a SpeedCal.