Before we dig too deeply into the wah/boost as being culprit, can you recreate the hum with any other fuzz or high gain pedal?
MechaGodzilla wrote:It's just running off a battery. The red + goes to the wah board and then I took the boost v+ from that. The battery black- goes to the stereo input jack and connects to the chassis ground point. The boost ground goes to the top left lug of the dpdt switch, which then goes to ground.

Should I just connect it to the chassis ground? Is there a problem with powering it this way?
My only concern here is the complex circuit the ground is facing. I would connect to chassis at one point (it'll happen through the stereo jack) and consider that a shield that should not be burdened with carrying any circuits. The ground/v- of each circuit board I would connect to the sleeve connector of the TRS with battery negative being on ring for the power disconnect. I don't know what function the DPDT switch is performing in relation to ground though, if it's bypass to fire an LED I would simply tie that (the ground feed to switch) into the sleeve of the TRS as well. Though if you've got a solid connection between the v- of your boost circuit and ground it's probably no concern.
I'd also hard wire the sleeve of the input jack to the sleeve of the output jack (and I'll use either jack as the sort of "master" ground plane, since battery powered stuff typically isn't really current hungry).
I'll admit, I would be more concerned about the current path in this area if the unit was powered from a PSU (which also fed the fuzz), but it sounds like that's a concern that does not exist here.
MechaGodzilla wrote:I don't know how but could it be a problem with polarity? I'm pretty sure the fuzz is PNP and the wah is NPN, which isn't an issue for the boost mosfet bs170 but perhaps they don't want to be friends for some reason?
You're talking about two different circuits, each inside their own enclosure and powered by their own battery, true? Should not be an issue.
Could be a high impedance on the ground plane between the two pedals, brought on by a bad or dirty jack or faulty cable. Have you a multimeter? Plugging cables into the wah, on into the fuzz, and out of the fuzz you should be able to measure the resistance between the sleeve of the first-most cable and the sleeve of the last cable and observe a figure as close to zero as possible.