Where to start?
 

I've got a 1996 12 valve, completely stock except fuel plate. Just looking for advice on what to start buying for performance first. Thanks for your time

fill out your signature it will help to know what all your working with. and unless your driveline is in great shape or you have money to fix it when it goes then dont throw too much at it.

Manual or auto? Intake and exhaust will help you get the most out of that plate.

Its an auto, im not really looking to throw a bunch at it, mostly just want some moderate power and torque gains

Problem with an auto is, moderate power and torque gains can put you out of commission in no time flat. That you have a plate already means you better be careful. If you don't have a trans temp gauge, get one ASAP.

Alright sounds good. What do I need to do in order to avoid this?

Towing is what will burn it up the fastest, extended WOT like dragging a trailer up to speed on the highway. But really, any time you're putting power down before the TC locks you're making heat in the tranny, and heat is the enemy. Any time you're putting power down after the TC locks up you're making heat in the engine, and their cooling is linked so you're getting hot either way. You could use an exhaust anyway to help balance your fuel plate power equation, and that would lower your EGT's a little- but probably only put a small dent in the issue. You could add a dedicated trans cooler, but really, there's no replacement for just building up the tranny to be able to handle more than a neutered Cummins.
I highly suggest starting with trans temp and EGT gauges to see where you're at now, and then you'll know both how you're driving habits and routines affect them, and whether the mods you do are helping or hurting the situation. Short of putting a stock fuel plate back in, you're as close to a safe baseline as you're going to get.

Alright, I appreciate your input and help, thank you!

Good luck.