The stock air box works just fine, all you would have to do is replace the filter with something better. A true dual exhaust is probably a bad idea especially for a inline 6 it won't give it any benefit, just looks.
A stage 2 Spec clutch is what I used which worked better than I thought with a stock resurfaced flywheel. Aftermarket flywheel would be awesome.
Just learn everything you can about the car before you go off doing anything to the car, research & read a lot everything you need to know has been covered on here a before and after pics would be nice as you fix it up best of luck!