Do mods lower value?

[ApathyCurve_imp]

As others have said, save the stock parts. Motorcycles, cars, whatever. Always save the stock parts. If you're going to modify a stock part with cutting, etc., buy another (Craigslist and Ebay are your friends) and work on that piece, not your original. In some cases, this can actually help close a sale. I once sold a modded Supra for my asking price because when the potential buyer carped about the body mods, air kit, and such, I pulled out the big box with all the original parts wrapped neatly in bubble wrap. He paid cash on the spot and drove away happy.

TL;DR - As long as you don't make irrevocable changes, mods don't hurt the value, IMO.