GuildFS4612CE, I'm in the same situation as you are. I recently acquired a FS46CE, which has the 1/4" wide pickup on rails that workedinwesterly mentioned. Mine's got the 3volt preamp with 2 AA batteries.
I haven't gotten to deciding on the tone of the pickup yet, but I'm pretty sure I'm going to be replacing it. The G and D strings are putting out MUCH lower volume than the rest of the strings, and the B string is louder than everything else, packs a really strong punch. So like you, I am looking to start over, fill the bridge, and cut a new slot.
My problem, though, like you, is figuring out what new pickup to put in there. One of the issues I've noticed is that the wiring hole for the pickup is in the center of the saddle slot, not off to the side like most newer undersaddle pickups require. So getting the wiring in there might be tricky. The solution would be to drill a new hole at the side of the slot, but getting that hole to line up with the channel going back to the preamp cavity might be kind of tricky, since this is a solidbody guitar.
The pickups I've been considering are the following:
1) L.R. Baggs LB6. Nice, simple. It's what (I think) I have on my Guild DV52. Just a passive pickup, no preamp, no batteries to worry about (I go into a Countryman DI).
2) L.R. Baggs Ribbon Transducer. Again, nice, and simple. Plus the saddle is not built-in with the pickup, so you can use different materials, or replace the saddle later without replacing the pickup.
3) L.R. Baggs Element. This is what's used in the Anderson Crowdster (look it up if you haven't heard of it - it's the guitar that got me looking into these solid body thinline acoustics in the first place). Problem is, the readily-available Elements come with the preamp built into the endpin, which I don't think would install well into the FS46 series guitars.
So those are my options I'm looking at so far. I like #1 and #2, because the guitar would be passive (I'd dump the electronics on the FS46 and keep the cavity empty) without having to worry about batteries running out. But I don't know which of those two would sound better for the solid body.
#3 is probably not going to work, unless we can get LR Baggs to give us a version with the preamp NOT in the endpin - but then, it would mean having an active preamp, something I'm trying to stay away from personally.
If your luthier comes up with a solution, I'd love to hear it. If workedinwesterly has a suggestion, I'd love to hear it, too. I love the feel of the FS46, and want to make it sound as good as it feels.