I cracked the case! or at least got the game to load. Add this to the data-final-fixes.lua file line 7~ish:
-- list of resources unavailable in quarries
local resourceBlacklist = {
["ground-water"] = true, -- bob's groundwater
["thorium-ore"] = true, -- bob's thorium ore
["vtk-deepcore-mining-crack"] = true,
["uranium-ore-patch"] = true
}
The ["thorium-ore"] bit fixes the bobs incompatibility, while the next two seem to resolve anything from vtk deepcore mining mod.