Hard one to diagnose. You know about the
color sequence so I'd suggest sticking with that.
Somehow, it seems more like coincidence that the machine died when plugging in the speakers. (Although, it having one of those PC speaker connections, I'm not sure if an Amiga would have any issues with the speaker outs being shorted, which is a possibility with those plugs.) I'd make sure the connector hack is good. Then go for reseating stuff (including the cpu card.)