Hmm..if the neck is dead flat you might want to try putting a bit of neck relief in there. If you do alot of bending, a little goes a long way. BTW, I recall you said the G string is the culprit who goes out of tune. Sometimes I put together sets with a different guage G, one thats a little heavier for lower tunings. I have found wound Gs seem to do better, but its been years since I messed with that sort of thing. I play rubberbands now. Lol Ok, lets address the honk in the room. Ill focus on the bridge since you mentioned its the bridge you dont like. Im monitoring this thru Beyerdynamic DT770s btw. clean sounds fine to me, its brighter than what I'm used to, but nothing crazy honky to my ears. Distorted sound definitely has more midrange, but nothing overwhelming. I'm sorry if you mentioned this before, but Im curious what you used for distortion. Im leaning on the distortion box being the reason for our honk, or perceived honk. Some color your tone in ways that will surprise you. Might also be the cause of our noise too, and it could be it or where its placed. I will get extraneous noise on mine, which have fully shielded cavities, but just by being in proximity to electronic devices (a computer for example). I often prescribe a good noise gate and eq. Guitars can be noisy things and pickup all kinds of signals. I picked up police transmissions once when I was a kid. An inline eq can remedy all sorts of problems with honky/bassy/bright tones. EVH used to swear by them. All that said...I dont think the bridge tone was crazy honky, a little but not overwhelming. The noise really aint bad either, I thought it was tolerable. One more thing...things that sound like shorts in switches and pots sometimes is just caused by a little crumb of poop getting in there interfering with the contact areas. Spin those knobs rapidly several times and sometimes that'll do it. Its sorta rare for me to see pots and switches that are actually goners.