It's your car, do whatever you want to it & don't worry about how its "value" is affected.
I originally purchased my '89 Saleen with no intention of ever modifying it because it was pretty much perfect as-is. Not to mention that in the late 80's there wasn't much in the way of modifications available for the 5.0 Mustangs & what was available was extremely expensive (anyone remember SSC shorty headers for $600/pair?).
However, once the market became saturated with 5.0 & Fox body specific parts, I went a little crazy, modifying everything but the factory shortblock & transmission. Of course when I sold it exactly a year ago, I didn't receive any compensation for all the $$$ I spent during my 18 years of ownership.
Now that I own my Saleen Cobra Speedster which is truly a unique vehicle, I've decided to be a bit more discrete in the modifications I add to it. The list includes full length subframe connectors & a strut tower brace to stiffen the body (it really needs them), an aluminum driveshaft, rear differential cover girdle, perhaps upper/lower rear control arms & a custom dyno tune for the stock DOHC engine. That's it.