The only way I would keep a Fox Body stock was if you had some kind of real time capsule. I mean show room quality with extremely low mileage or a limited or special edition car. With that said, I really don’t think you will be hurting the cars value by doing some tasteful mods. And you will definitely be increasing the fun factor. And like was said earlier, if you ever want to go back to stock, you can. Just save all your parts.
I've been debating finding myself a near stock '86 GT with t tops or an 87-89 GT and doing a full stock Resto. If I had your car, 10-holes new headlights, buff and wax and then go though the underhood and restore/replace with oem Ford or Motorcraft parts.
Keep the stock parts and try not to do anything that can't be undone. Don't mess the interior up. And if you must lower it, dont go too low. Do it right or you'll *uck up alot of things like poor ride quality, poor front end geometery, tires rubbing, bottoming out, etc
That 'thing' is real, I remember when I only wanted to fix the drivers seat in my stang, before long I had the whole interior out and was replacing the ac/heater core, dynomat from dash board to taillights, new carpet ect, by the time I got it back together I couldn't afford to fix the seat!