Hey I am making an awesome frankenstein monster guitar with tons of hot rod add-ons to it and I was wondering if it would work to put a DIY single coil sustainer in the middle position rather than neck. I can imagine magnetic field issues from them being a little closer together, but I am rather ignorant about this stuff. I also want to stick a neck pickup in, so would that kind of wiring be too much and suck tone? Thanks in advance.
No. I think the Sustainiac page has a FAQ question that specifically deals with this. The middle position will give you a squealing mess. I have a with a sustainer driver and a single-coil-size rail humbucker side by side in the neck pickup ring:

The sustainer is NOT located in the control cavity -- there's a separate rout for the Fernandes circuit board and for the battery box that runs it in the back of the guitar, and the two miniswitches that control it are out of the way behind the Floyd.

On this guitar, volume control nearest the Floyd has been moved out of its normal LP-quad position and closer to the bridge/bridge pickup. It's also become a master volume. To the left of that is a master tone and to the left of that is a Buckethead-style kill switch. Below that row, one knob is a push-pull that controls a chandler Tone-X, a sweepable active mids boost (about 16 dB -- the battery for that is in the control cavity), and the other is a Sustainer Intensity pot.

The neck pickup used here is a DiMarzio Fast Track II, about 18K worth of strat bridge pickup (ordinarily), but used in the neck of an LP, it's both more focused than a standard humbucker and quite a bit more powerful than the bridge pickup. Less of the traditional LP neck-position mud on the bottom end. It's a great lead pickup in that position.