This is a long shot, but...
Have you made sure that you've tightly screwed in the motherboard screws to the case, once you put the motherboard back into the case after replacing the battery? I've heard from an ex-Amiga repair guy here in Toronto that the A4000 mobo was designed to be grounded through the case itself and the grounding "path" was through the screws. I've never confirmed this though, but you never know...try it and see. Tighten those screws and fire it up.
