i know you mentioned you checked all the connections, harness's etc. i assume you checked the main merc harness at the rear of the engin. the one about 1 1/8 diameter with a hose clamp on it. i don't mean to insult you in any way shape or form however those plugs will do weird things if they go bad and or are get seperated. seems like you may have done something near or in the area of what you recently did when it fired for you.
This is exactly where I would start. Clean up the connections and spread the pins a little. Clean the inside connectors as well. We just had this exact problem on another boat. It has happend to me on two outboards as well with the same connector.
