The skegs I used were thicker than what were on the drives no I have a small step from one to the other, I cleaned up the weld and I am not sure what to use to feather the two different hights. Bondo, marine tex, JB weld ? .. What will adhere to the alum best ? Any suggestions

Marine Tex should work I would think.

I had a two part putty called QuikSteel that was fantastic. Dried so hard you could drill and tap it. That would also work IMO.