Just my opinion, but if you want to stay fairly stock, don't waste your time with all the little things. Forget the catted h pipe and headers, you'll see absolutely no power gain with a stock engine. If you do the better intake, it's not going to yield you much power at all without also doing the full round, which means bigger injectors, better heads/cam etc. Don't bother with that stuff, including the mass air meter until you are ready to get serious.
Like touched on already, there are a lot of inherent fox body weeknesses that need to be touched on before you start modding your car. My buddy has a heavy ass 89 convertible with 237k miles on an original longblock, original stock heads, stock intake, etc. he concentrated on all the other stuff.
your aod is severly holding you back, a shift kit is a MUST, I would also spring for a torque converter, etc etc. the more you work your aod, the better off you'll be. I would get gears too, but if you are not addicted to going fast, I wouldn't go beyond 3.55's or 3.73's Good rear control arms such as maximum motorsports are essential. Combine those with some good lowering springs/shocks, and you'll have a good efficient machine that handles great and performs great without spending butt loads of money on mods