If it works as expected in bypass, and you're hearing a processed Rat sound, however attenuated, I'd let the switch be for now and assume it's a mixing issue... especially since Robert indicated it's a problem.
You definitely have more wires than you need, but they might be functional as wired. It's hurting my brain to think about, so I'd like to put that off.
One thing you can check is disconnecting the SD-1's board-out wire and see if the Rat side then functions as expected. If so, that's another indicator that it's a mixing problem.
If it turns out to be something more than a mixing thing, I'll show you how I'd have gone about wiring that up. For future reference, Aion's "legacy" boards would have been a better option there since they have polarity protection and all powering filtering on the mainboard... instead of moving bits onto a daughterboard. Of course, you have to source your own parts for those, so there's always a trade-off. I feel like I have to mention that PedalPCB also puts them all on the mainboards.
