I've got three Fenders, in various degrees of modded-ness:
I've got a '74 Precision that was modded when I got it: replaced pickups (Hi-A), replaced pots, Hipshot Ultra-Lite tuners swapped in. It also had a new pickguard, appears to have been painted, and was re-fretted at some point, with the back of the neck and the fingerboard stripped and re-finished with thinner lacquer. I don't always consider cosmetic changes to be mods because they don't usually result in any functional change, but the neck on this one feels different than most other 70s Fenders I've experienced due to not having the thick finish everywhere. But this was all done to it when I got it, and I haven't changed anything since. It is a very nice bass as it is; I have no idea what it would have felt like or sounded when it was stock.
I've also got a '92 MIM Precision, which also has new electronics including Seymour Duncan SPB-1s. I had a set of Fralins in it for a while, which I got just to see what all the fuss was about, and I loved them, but I ended up putting them in a different build. So I got the Duncans because they seemed like the same type of pickup (vintage-style), and so far I'm happy with them. I find the stock MIM pickups less clear, although they are certainly loud and punchy. I also put Hipshot Ultralites on that one too, after feeling what a difference they made on the 74. Also, the original tuners were pulling out of the headstock, which I have never seen on any other Fender.
Finally, I've got a AVRI 62 Jazz Bass, which as far as I know is entirely stock, except that I did put pickup covers on it. While that may or may not count as a mod, I did it because an original 62 would have had them.