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I just started this summer project with my Epiphone Les Paul Special II, making some kind of overhaul by changing the nut, the bridge, and the electronics.

I took my guitar completely apart and now I am plagued by questions. I see that there are some areas that are not completely leveled or smooth in the place where the neck meets the body (it's a bolt-on). Should I sand this so that it's leveled and smooth? Could the guitar lose the capability of being in tune and have good intonation if I sand this?

I got another surprise too, there's this cable that comes from inside the body and it's labeled bridge ground. Isn't that dangerous? I mean, have I been at risk by playing this guitar while having it grounded to the BRIDGE? What's this cable doing there and what should I do with it if I'm planning to change the bridge and the electronics?

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    The ground wire is just there to provide ground for your guitar innards. Its usually attached to the bridge, or the one of the string ferrules. Without it, you'll more than likely get a large amount of ground hum out of your guitar, every electric guitar has this, It's not dangerous unless your amplifier has serious electrical issues or you plug your guitar into live power outlets. If you upgrade your electronics, you'll need to provide ground. So its best left in place! – Matt D Jul 11 '13 at 1:30
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Sanding there will not hurt as long as you do not over do it and change the angle that the neck joins to the body, and thus the action, in fact light sanding to smooth the area could possibly help a tad with sound wave transfer from the neck to the body, enhancing the sustain and tonal qualities, which is one of the benefits of the way (for an example) the Gibson Les Laul guitars and others, have the neck bonded to the body. However, on the other hand, I have an old old Fender Stratocaster with a bolt on neck (like all strats) and it is my fav. electric guitar. but back to the topic, a good joint at the neck / body area should be beneficial in some ways. The more you lower it the higher the string action would become, and if the angle there changes significantly, it could become impractical or impossible to set the action to a good heigth. But as long as you sand lightly and evenly it should be fine.

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