It seems that I have nowhere to else to approach anymore but here. Recently, I bought a second hand PRS SE Singlecut with Seymour Duncan Jazz and JB pickups installed inside. When I got the guitar, I was HORRIFIED to find that the tone was extremely muddy. Thinking that I could be due to a bad setup and old caps, I send the guitar for a full set up and changed the caps. However the guitar still sounded horrible and muddy.

I then took my Dimarzio Liquifire and Crunch lab pickups from another guitar of mine and installed it on my PRS, changing the pots at the same time. After changing both the pickups and the pot, the tone still felt extremely muddy, in fact even worse. Can anyone give me ideas on what could be wrong?

Well, it's pretty much impossible for us to diagnose your setup over the internet. But there's pickup height, string height, etc. to check.
However- given that you rewired the whole thing and used different pickups, it may just be that the guitar is a dog. A JB is about as far from muddy as you can get, and there's really no reason you should have to get silly with 1meg pots or anything with it, so unless there's something very unusual going on, it may just be the guitar.
One that sounds crappy no matter what pickups or electronics go into it. As with any product, sometimes a bad one leaves the factory and no amount of alteration can fix it. With guitars sometimes it's a neck problem or the batch of wood was just unusually bad.
Did you check your amp? Might seem silly, but I've definitely hit a wrong switch or accidentally turned a knob before and got it all out of whack. Just a thought.
'Please help' is not a good name for a post. Nobody knows what is needed. For all we know a string went flying and scratched you're cornea or a tube shattered and you are cocered in glass.

So why not say 'guitar not sounding right please belp' much more effective.
WTLT 2014 GG&A

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youre just being a jerk man.

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You're turning your tone knob up, right?
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