Ok, exhaust wise do the following, first get some nice long tube headers, not those wussy shortie ones. They are harder to install but offer way more power. I bought my flowtech set for my mustang for around $120. Just do an H-pipe setup and run the exhaust into some Flowmaster mufflers and end them with some nice stainless tips of your choice (don't get chrome unless you like rust color within a year). Install the headers yourself, then the exhaust should run you about $400 for a decent 2.5" all the way back. Plus about $150+ for mufflers. A good exhaust costs money but is well worth it.
On the subject of paint, either it will cost alot or a little a good quality paint job requires ALOT of work, which entails removing everything you can, prepping it, priming it all separate, painting the hard to get areas, then assembling it and blasting it the final color.
Pedals and clutch setup should be a cakewalk. It should bolt in easy, you just gotta remove the dash to do it easily
. and the clutch is just a plain hole in the firewall and its cable operated so its not bad at all. The thing with the linkage is the thing that is gonna get you. You can't extend the linkage on a T5 transmission. The shifter is directly bolted to the transmission. But if you want I can take some dimensions so you can tell if it will line up. I believe the driveshaft doesn't need to be modified at all. The t5 and the AOD share the exact same tail spline size and the AOD is as long as a T5.