Hi Eric, A couple of things to keep in mind (I'm sure you already went over these, but just in case): - Merge is expensive, make sure to merge your groups at once instead of add part by part through multiple merge operations. - Transfer weights from a single cage mesh works way better than from small/partial parts, if you don't have a cage try merging everything together once and use that as source for your weight transfer. - FreezeM all the things! looks like you're dealing with expensive operations (merge and gatoring) + dense meshes, FreezeM between operations makes a huge difference!
Maybe you can share a pseudo-code/outline of how you're approaching this, that way would be easier to spot possible sources of slowness. Cheers!