I bought a 99 trans am that somebody swapped the stock auto for a t56. But didn't change any wiring. I was told that's the reason my reverse is destroyed. Anyways I would really like to switch to a built 4l80e. Should the stock wiring just plug in? Or is there something else I need to do

 

On a 99 you will need a segment swap done to make it shift correctly

 

And a wiring adaptor kit. Sold by Speartec and pcmforless. The "segment swap" mentioned by cable1, refers to the pcm tuning. You will need to download a portion of a truck tune to allow the fbody pcm to control the shifting f the 4L80e.