2001 Yamaha 60 hp four stroke backfiring issues

[climb29028]

I have a 2001 Yamaha 60 hp four stroke that is backfiring at idle and at throttle. When I give it throttle under load it hesitates a bit but then runs fine. I just had all the carbs completely cleaned out and it's still doing it. The mechanic who worked on the boat noticed that one cylinder was not firing but later it would fire then another cylinder would stop firing so he thought it was the carburetors (which I thought was strange). Obviously it wasn't. Apparently I have great compression in all cylinders and the plugs all look good. I use good quality marine gas and use a water/fuel separator. Could this be a timing or electrical issue? Any help or suggestions would be greatly appreciated. Thank you.

 

[99yam40]

back firing to me means blowing out of the carbs.
to do that the spark has to be happening while intake valve is open.

spark timing off or
intake valve open for some reason when the spark happens when it should

 

[climb29028]

Something to consider. Thanks.