Ok while removing the undercoating on the hump I put a hole through it with my scraper. While looking at it I noticed the metal is thin, but not rusted though just surface rust. What is the best way to repair this?

Weld it.

If you do not want to weld, POR and glass.

If it is thin enough to poke through fairly easily, I would buy a new trans hump all together and replace the whole thing.