Looks really cool!
I would go with a Sustainiac Stealth or Stealth Plus, because you'll have choice of bridge pickups. Wiring might be a little trickier, but the instructions that come with the kit are excellent. Not for the faint hearted, but still manageable if you know what you're doing with soldering. The circuit board is also smaller, so you won't have to rout out half of the back of the body, so that part of the installation will actually be easier.
If you know exactly which pickups and switching you're going to use, Allan Hoover at Sustainiac will also provide you with a custom wiring diagram that will show you exactly what needs to get wired where. He'll also advise you if you're proposing a pickup or switching combination that won't give you good results. This is a huge advantage, versus trying to reverse-engineer the Fernandes unit if you want to change the bridge pickup.
All magnetic sustainers will automatically bypass the pickup selector and switch to the bridge pickup when the transducer is active in sustainer mode. The middle pickup is not an issue, because it won't be in use when the sustainer is on.
A humbucker in the middle is actually a great sound. One of my guitars has a JB in the middle with series/split/parallel switching, and it's super-versatile. It's a very open sound (especially in parallel mode), a little more mellow and with more depth than at the bridge. Put a hotter, more obnoxious-sounding bridge pickup in there, and you'll have a lot of tonal options.