Best way to fix the roof, is to remove the entire lining. It's a bit of a pain in the arse, but once it's out you can peel off the material, and glue on some new material of your choice.
And the auto... well, you're looking at quite a bit of money if you pay someone else to do everything. Stage 2 shift kits will set you back around $400 installed with a 1/2 servo piston, and will only make a slipping gearbox fail sooner - so you're looking at just dropping an entire 2nd hand transmission in and getting that kitted. Rebuilds are expensive