Re: Magnet swap to fix JB's muddy cleans
Many JB users either split the JB or switch to neck pickup for cleans.
JBs can be muddy, most people who like them refuse to use guitars they don't work in, so there's a myth they can't, or that guitars that don't work with JBs are useless. Usually the upper-mid spike dominates so thoroughly that any excess lower mids doesn't get noticed...
Gregory's suggestions for magnet swaps are good choices. Another option is shorter screws under the wound strings, to tighten things and improve attack/bite. 0.5" hex head are very popular for the task. But that may not be enough, as loose JB is usually lower mids, not excess deep bass.
You could also look at a Perpetual Burn, if you want a more precise, less over the top JB.
My Ibanez RG570 that was muddy with a JB sounds great with a PATB-1b Original Parallel Axis. [I wound up with the JB with A3 and 3 hex screw polepieces as a neck pickup, where it is ridiculously fat but gets a wide variety of unusual neck pickup tones.]