If I were to actually buy a very clean, lightly modded foxbody, I would probably make an effort to demodify it and return it to stock. This is actually part of my plan as I seek out some sort of Fox/Sn95 to purchase after my car is finished. I doubt i'll find a stocker, but if I found one with bolt-ons, I might be crazy enough to return it to stock. A no-brainer if the car is something like a Fox Saleen, or a '93 Cobra, however I actually think if I found an LX convertible with a 93 cobra intake on it, that I would put the HO intake back on.
The nice thing about my current fox is that I know i'm never going to sell it. It's been 23 years, and the sentimental attachment pretty much mean it's mine forever, so it stops me from thinking about what mods I should or shouldn't do. It's freedom of sorts and I could care less about perceived value of the car, although it's flattering in a way when I used to get people try and make offers on it when I went out for a drive. However, buying a collectable fox like a 93 Cobra, I could see myself selling that as values appreciate, especially if it gets to the point where they become a $100K car like a Boss 429. I feel in that case, I couldn't modify it, and needed to locate NOS parts for it. I would also feel bad driving the thing.
I remember when these things were a dime a dozen. You could get 50-75K mile examples in near stock condition for $5-6K. A driver was a $1500-2K car that didn't need much other than paint and some interior trim. Parts cars/rollers were $500-1000. You could drive down the road and see at lease one on every used car lot. I spent my teenage years drooling over $7-8K 90-93GT's with 50K miles, and had to "settle" for my "cheap" $4500 LX with ~45K miles on it. Now I find a 93 Cobra for sale for $25K and think to myself...maybe I should buy this?