I've been seeing some craziness in listings on the 'bay lately. This is just my opinion, and you're of course free to argue.
Custom / Customized / One-off - these are terms that should be used only when something was done to a guitar on the FACTORY / employee level. On the factory level, this may add value to an instrument.
Modification / Mod - this is something that is done by the purchaser / end-user of an instrument. Any part that is changed (besides strings) is a mod. I see "100% original with strap locks & locking tuners added" - this is no longer original. The more major the modification, the more it decreases the value of an instrument.
Upgrade - is in the eye of the beholder. As a collector and player, I like to buy guitars in their original factory specs. When looking for a different sound, I'll use a different guitar. A strat with an "Upgrade" to humbuckers/noiseless pickups to me is not an upgrade - it's a modification. Fine if you want to do it, some of those pickups are great, but it's not an upgrade if you like single coils. I feel the same when going to name brand pickups - what's an upgrade to one person may not be to the next.
Thanks for tolerating my rant.