This one's gonna be a little long, so bear with me.
I have a Japanese Jaguar that is about six years old and I have recently attempted to give it a more 'professional' setup. Here's what I've tweaked so far:
Straightened out the neck (there's a little relief in it, but not much)
I put some metal washers under the truss rod nut because it seemed that I was turning it too much with no noticable adjustment. I thought that I may have over-tightened it in the past and compressed some of the wood in there.
I shortened the saddle screws (not the height screws). The low E and A strings were resting on the ends of the screws.
I set the intonation.
I added a string mute awhile back, which required me to drill a hole underneath the bridge.
I added a Buzzstop almost as soon I got in in 2003.
I put on Fender Bullet 11's. I can't remember if I ever used Bullets on this guitar before.
Cleaned out some of the gunk in the nut.
Phew. I think that's everything. I just want to make sure I have it all covered. The problem(s) that I'm having now is that something is buzzing/resonating when I hit the strings. It sounds like a really metallic harmonic or a spring resonating. It's most prominent on the D and G strings. I can hear it when it's not amplified and when I do use an amp, it's REALLY noticable. It sounds like it's coming from somwhere near the bridge or even behind it. In order to try and troubleshoot this, I've put silicone around all the springs (including the trem) and anywhere there is metal to metal contact in the trem/tailpiece. I also tried putting plastic under and between the saddles, but no luck. I'm at a total loss as to what I did to create this problem. Any help would be appreciated; I would really like to fix this myself and not have to take it anywhere unless I have to.