hey bro. first and foremost welcome. as odd as it may sound the woolly mammoth isn't really that easy of a build, especially due to the large number of pots for the offboard.
in any event, i took a quick look at your wiring and it looks fine. to answer you question about where the ground wires from the pots go it's much easier then you may think or realize. just attach them to the jacks. in fact you can actually connect the ground from the wool pot and run it to lug 1 of the output, then have one wire going to one of the jacks.
when it comes to understanding circuits and building grounding is one of the easiest and most over looked concepts that always gives people hangups. think about it like this, all your grounds are going to your enclosure, this is due to the jacks. you know how your jacks are metal, and you have a ground lug on the jack? and since all your grounds are connected, if you need to run a ground, just put in on the jack and you're golden.