You probably already know it but grounds are a big deal on a battery relocation. I was having a charging issue that ended up being a missing ground to the frame in the back of the car, even though the battery was tied directly to the back of both heads.
Secondly I thought it was fixed because my voltage was much better but realized my battery disconnect didn't work, so I ran the charging wire from the alt all the way back to the battery side of the switch and it's better than ever. The lowest I've ever seen it is 13.5 volts.