I have never had a custom instrument made for me, but I did have some modifications done to factory instruments with mixed results. These were nearly all electronics mods, so easily reversible. The one that comes to mind that REALLY disappointed me was the addition of an Audere JZ3D preamp to my 1975 Jazz Bass reissue. It changed the character of the bass, even with the controls flat (less bottom end with the EQ flat, and slight compression), and added a huge amount of control options that I never used. Being a lefty, the one thing that annoyed me most, though, and which I hadn't taken into consideration when ordering the preamp from Audere, was the controls all worked in the opposite direction of what I was used to, including the pan pot! It worked so counter-intuitive that I absolutely hated the bass and stopped playing it entirely. It's a great bass though, so after sitting in a rack for months I decided to have it changed back to passive, with a regular VVT setup again, but I did have an active bass boost added - because I decided the only controls I ever use on an active bass are bass boost and high cut. It's absolutely perfect now.