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Can I get the serial number please?
I'm suspecting ignition problems. Do you have a spark tester? If not get one from any auto parts store. Set it to 7/16" gap and check for good spark. Make note of which cylinders aren't firing properly. From the back of the engine looking forward the #1 is top starboard (right) #2 top port (left).
I would also look into getting a fuel pressure tester. Many of the larger chain parts stores will rent/ loan you one.
Do you have a voltmeter that can read resistance?
Let me know about the spark asap.
I'll check back tomorrow.
I'm going to give you the fuel injection chapter as it is was to cumbersome to try and troubleshoot step by step here. Follow the instructions. You will need a fuel injection tester. You can get one inexpensively at a discount tool store such as Harbor Freight.
Your ignition seems OK. Same with the kill switch.
Have you tried to run the boat since the regulator was repaired?
You can check timing with a timing light and we already did a ignition output test.
Run it and post back how it does.
To check voltage you need a special voltmeter and peak reading voltmeter. I wouldn't bother measuring the coil resistance as it is highly doubtful all 6 are bad. You can remove the kill wire, the black yellow, at the switchboxes. The top row if connections, red, blue, white black and black yellow.
Do you have an inductive timing light? You can check ignition with it as well.
Crank the engine and check for spark that way.
The stator is usually the weak link in the ignition, here we can do a few tests with an ohm meter but still rely on the peak reading voltmeter.
Do you have a good volt/ohm meter?