Welcome to the site! Good to hear the Pontiac gene is alive and well.

As far as your mod plans, I'd stick with a standard paper filter, keep the stock exhaust and just get a 3" catted downpipe from ZZP, replace the plugs with the stock ones and the cheapest wires you can get. Trans. cooler is a plus. The money you save on those will go towards some real mods in the future. Clean the MAF and the throttle body too. Do a pan drop/filter/fluid change on the trans. DO NOT FLUSH IT!!!! Might be a good time for a Trans-go kit as well since you're in there. You can grab one from tripleedgeperformance.com. Dave will set you up with what you need. Lots of info on his site as well.

Then go over the entire car and replace things as needed. Check all the struts as they're likely about done by now. Basically get everything replaced that needs it so you have a solid base to start with. No sense modding a car that is always going to be broken down

I'm sure you've seen this thread, but if not give it a read- Safely Modding Your 3800 Powered Car!!