Question have you tried the "wink blinky" to see if it's throwing any codes? Our motor actually does store electrical fault codes but they are simple. The light blinks a certain number and the owners/maintenance manual has the decipher to the codes. Someone on here had the plans to build one for pennies of what a yamaha part cost...was a few years ago though.
I would also put a timing light on your wires, throw someone in the back and run the boat to see if it is spark related.