This is my 2013 Sterling Ray34CA, of which only the body, bridge and preamp are still original. The pickup is a Nordstrand MM4.2, the nek was custom built for me by a Dutch luthier and I've replaced the not very pretty tortoise pickguard with a black one. I'm planning on replacing the preamp too.
And then there's my 2001 Fender Standard Jazz fretless, with a Gotoh 201 bridge, De Gier prototype pickups and a black pickguard:
I've also replaced the pickups in 3 of my other basses, but that isn't very visible so for me doesn't count as an actual modification. Just an improvement.