I have a 540R which is almost the same as the JS1000, I too had a Fred in it which I quite liked but I felt I needed a bit more breadth.
I tried 3 BKPs in this guitar and they all sounded bigger but in different ways:
First was a Nailbomb, which is a lot more aggressive than the Fred. It has good mid range and great harmonics that work well for Satch stuff, notes really jump out, but I thought it was a bit too Metal for this guitar.
Next a custom pickup that Tim made me, the closest equivalent would be the Holy Diver, and that was good. Very smooth and powerful in the mids but without the aggression of the NB, maybe the bass was a bit much though and I wanted some more air (this may be due to the double row of screws and symmetrical wind on this pickup, the Holy Diver would probably fix that).
Finallly I got a VHII set and I'm very happy with that. It doesn't sound like Fred, it's more open and airy, it has good mids but is flatter across the sprectrum.
So as you can see none of them really sound like Fred.
It's up to you to decide more specifically what you want to change, the tonal balance? output? air/punch/harmonics?
One last point, another option that is rarely mentioned is the Emerald. Tim described this to me as a fatter and slightly more powerful VHII. That sounds like a winner to me but I haven't heard of anyone using one in a bolt-on :?
