Currently only the WD500 has an OS, the others are just storage. I can erase the entire disk from the top (highlighted) and that should clear out any traces of OC including the post-install patches, right?
Correct
Do a clean install of Mojave (not TM backup), replace the GTX 680 (flashed) with the RX 580 (non-flashed), reset NVRAM and disable SIP, install MLOC to the WD500 drive and bless.
Is there anything I'm missing, e.g. OC settings?
I think you better just use RX580 but not the GTX680. Boot screen is not required for Mojave installation. And the Mojave installer may not recognise the GTX680 as a Metal supported card.
But yes, once you get Mojave running, you can reset NVRAM, disable SIP, install my package to the WD500 ESP.
Anyway, you better mount all drive's EFI partition one by one, and check if there is any OpenCore stuff remaining.
It's more than once that people asking for help (e.g. can't remove OC, or can't update OC, etc). End up because there were multiple OC installed onto different drives. Therefore, their cMP keep running from a "hidden" OC copy.
Before you do anything, you better check all EFI partitions, make sure they are clean.