1) Profet23 makes great cases. I usually deal with him on Reddit, but I'm like 90% sure he's on GH too as the same username.
He made this case for me.
2) It depends, mainly on the key profile. If it's DSA, it'll be super easy to get matching modifier keys from PMK. If it's SA, it will be a little harder to match, but possible, also from PMK. I think you can safely rule out cherry profile keys. As far as I know, there isn't a cherry profile set that would have all of the correctly sized keys that match the ergodox's needs.
3) I'm certainly not that much of an expert to answer this question accurately. As far as I know, no. But I admit that I haven't really gotten very far into messing with the firmware beyond customizing my layout.
Also, quick mod: Don't go for PCB mount. I have yet to see a PCB mounted ergodox that didn't have a low-quality case.