Hi Liam, where did you measure the alt output? It may have changed but I was under teh impression that smart charge did not affect the alt mechanical charging ability. I was under imprwssion that there was still a regulator in the alternator, could you check voltage and current output at alt lead? Have you reset the battery sensor if it has one? Is it an AGM battery? Can you check the resistance of the can lines, should be around 60 ohms, can you scope can line and check signal out put?
HTH jim