Ok, so SLR uses DeoVR, and I noticed DeoVR was having the same exact problem as SLR.
I found where DeoVR stores button configs, they were in the registry under HKCU/Software/DeoVR. I deleted the keys and I now have the trigger button working again, which is great.
Then I tried to customize my controls again and found that only the trigger button and the thumbstick were being registered. The touchpad and the grip button were not working at all. I tried playing around with controller configs through SteamVR controller bindings, like changing the touchpad button to use TriggerButton, but that still doesn't work (looks like TriggerAxis is what works)
So... yeah, WMR controls are currently screwed in SLR/DeoVR, hoping one of the devs sees this and can provide an update
Thanks