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Oh man, I just can't be fucked with him anymore, I'm done with the guy... I'm gonna put the guitar away for six months and come back to it fresh next year...
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This. When I got my Koga-Miyata refinished it took absolutely bloody ages longer than I expected, the painter didn't paint the gold outlines on the logo as "it wouldn't have looked right" and then when it inevitably got its first chip I discovered the bastard hadn't stripped the frame before painting it and just whacked it on over the old paint. WAC.
That being said once I got over the annoyance about it I've come to love it and even though it's not exactly as I thought I wanted it to be it's still bloody brilliant!
I'd let the dust settle and see how you feel about it after a while but leave it out and play it!
Also; poor form on making the mod to the bridge without consulting you first but if it actually improves the intonation and playability of the guitar I think in the long run it's a good thing (again, when the dust settles you might be glad of it). As you've said before it's not an original unmolested example so might as well have it sound as good as it now looks!!It does look incredible, extraordinarily tasteful :)
Nahguavkire
By that logic if someone who owned a boutique built s-type or similar took it to him for a set-up and he happened to notice that the jack socket was not on the scratch plate he'd add one in there because that is where you'd normally expect to find it and it's quicker if he doesn't have to wait to ask the client?
The finish of the guitar looks amazing but if I were in your shoes I'd be expecting a like for like replacement, even if you are planning on putting another one on.