Custom - Some people were telling me this might be too bright sounding in my Charvel?
Those people are wrong IMO. Great sounding pickup, lots of bass and output, punchy, but looser on the bottom than a JB or D-Distortion style pickup. Depending on the amp, you might find it perfectly fine, but with a boost that loose bottom is a non-factor. One of my favorite pickups and one that I didn't think I'd like from online descriptions until I tried one by accident (came in a used guitar I bought). It's not brighter than a JB to my ear.
JB - Some say to use a 250K volume pot with the JB
A 250k volume pot reduces the brightness of any pickup, including the neck single coil. Since you only have one volume and no tone pot, it's still going to be a bit more on the bright side compared to a strat for example, where the signal might have 2x 250k pots or even 3x 250k pots in the signal path depending on your pickup selector position.
In short, if you find a JB too bright in other single-volume guitars, try the 250k pot. I personally don't care either way and I'd just adjust the treble/presence on the amp but it is technically a different result. Either way we're talking about a tiny tiny part of your signal chain here, your amp and speakers will have a much larger influence on this than the pot itself. You have lots of nice cabs and amps so I'm sure you could find a happy sound with either 250k or 500k pots and a JB, so what single coil you choose may influence this decision more than anything.
Tone Zone - Some say might have a boomy low end which I don't want
I've heard this before and I'm not sure where it comes from. It's certainly tighter on the low end than the Custom or something like an Invader. It has a good amount of low mids which adds some punch especially with Marshall style amps.
The main thing about the ToneZone is that it has "dual resonance" coils. Essentially this means that each coil of the humbucker is wired differently, as opposed to something like the JB which has both coils about the same (there's always a little bit of variation but it's not intentional). In the case of the Dimarzio, it is intentionally done so that one coil is different from the other with the goal of creating more harmonic overtones. How well this works is in "Ear" of the beholder. I like it as a change of pace from my many JB equipped guitars.
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I see from your signature you have many JB equipped guitars. My advice would be to try something a bit different, like the Tone Zone or the Custom. The Gravity Storm has the same dual resonance thing as the Tone Zone but the specs for each coil don't look that different online, but I haven't had one so I can't really comment. Even if you don't like the TZ or Custom you can at least use that as a basis to describe what you might want in the future or understand other online threads that compare pickups.
Quick mention, I see the 5FX has EMG's in it right now. Have you tried the EMG85? If it has recent EMG's it's as easy as turning a few screws and connecting the new pickup, no soldering necessary. The EMG85 is much thicker sounding than the 81 to me and while I love them both, the 85 is my favorite EMG bridge pup. I remember in your other thread you wanted a thicker tone so that's why I mention it.
I also have to mention that unless already modified, your 5FX will require either routing (please don't) or modified single coils to fit into the neck position. The factory Jackson J100/J200 single coil or the EMG SA fit fine without modification, but pickups with the "triangular" bottoms like every one you listed will NOT fit. You can custom order ones that do though, but I've never done this myself so someone else can weigh in there.
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Single coils:
Cool Rails
Lil 59
Classic Stack Plus
True Velvet
Those are extremely different sounding pickups. What is your goal for the neck pickup sound?
Rails and Lil 59 will both sound closer to a full size neck humbucker if wired in series. I didn't love the cool rails myself, but the lil 59 is very decent at classic neck humbucker overdriven lead tones, or really full sounding jazzy cleans. With a good amount of distortion either pickup can do the neck hum shred/sweep stuff.
Classic Stack Plus is a hotter single coil sound and gets bright and gritty, especially with no tone pot (unless you added one, please don't...). I like the way this one sounds a lot myself but I like gainy single coil lead sounds. More mids and bite than a traditional single coil sound. I liked the Custom Stack Plus (STK-S6 and STK-S7) even better, which is even a little louder. These are all noiseless/stacked designs.
True Velvet. It's a classic single coil sound, super low output, scooped out mids. Bright and spanky by itself. No quack because you don't have a middle position pickup, which is why I personally wouldn't use this but that's all up to your preference. This is a true single coil, no noise cancelling so it'll hum quite a bit under gain.
That's basically the full range of single sound options. Narrow it down more and maybe we can help you pick what you want better. For example, if you want the vintage single coil sound, you'd be comparing the True Velvet to the Duncan Vintage Staggered or BKP Slow Hand. But comparing a True Velvet to a Cool Rails is like apples and oranges, extremely different sound and purpose.
See my notes about regarding single coil fitment into the 5FX, all of these pickups will NOT fit without modifying the pickup or the guitar body.
