Ok so I'm trying to get my Kelly in perfect shape after a set up and have it feel and sound like a tech just had his way with it.
I'm gonna have it tuned to Bb and just got a hybrid D'Addario set of 13-56.
I've heard a lot about adjusting the truss rod and stuff but if anyone can give me a case specific to do list I would greatly appreciate it. I'm a little wary of getting inside my guitar in that way.
I'm trying to get it to sound like Cannibal Corpse's guitars but I'm going to assume this will take care of itself after the strings, set up and tuning are all completed.
Cannibal corspe play in Eb standard
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    Quote by Fat Lard
    I like semen, so what?
    Having your guitar set up well is great, and will allow you to play to your potential... but honestly has nothing at all to do with tone. The entire guitar itself has very little to do with tone compared to the amp/pedals.
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    Not all Cannibal Corpse is Eb, they go as low as Drop G# now (evisceration plague)

    You're going to want to get the jackson owner's manual off of their site (if they have it) if not then look up a basic truss rod adjustment guide, you;re going to have to compensate for the lack of tension on the strings, not a hard thing to do. Then you'll have to adjust your intonation, just make sure the open string is the same not as the 12th fret, if it's not then you'll need to adjust your bridge saddles, forward if it's flat back if it's sharp (if I remember right) that's pretty much it. As for tone coming from your amp, yeah it does, a setup won;t change your tone, it'll just make your guitar easier/possible to play at that tuning. Actually I lie, it might affect the timbre a little, but nothing major.
    Those strings are not going to fit in your nut. Have a tech/luthier cut a new nut (save the original in case you want to sell the guitar later, because most people do not play in Bb), and while he's at it, set up the guitar. This will probably cost you $100, but that's still cheaper than buying nut files and a lot easier than trying to do it yourself.