Have read through the whole thread now and first have you checked spark at all plugs with a timing light or with the plugs out and grounded?
Best is to check with a timing light and at the same time you check that it is firing at right time at each plug.
The timing light will work at 2 and 4 stroke but the tach if it has, shows wrong RPM if it is made for 4 strokers.
When checking spark with the plugs out and grounded you do not know if the spark is good enough to fire during compression.
If doing it with plugs out you have to check that it manage to jump spark at least 1/4 but 3/8 or up until 1/2 in would give sufficient results.
Imaging you have multiple issues, you have to verify spark at each plug under compression or in air it should jump spark 3/8 in.
The ignition system has two CDI modules and they can interfere with each other cause it is a blocking diod built in.
Also the rectifier can cause ignition issues.
Try with the rectifier disconnected.
Nordin, Thank you for the feedback.
I checked the spark on the motor and all of the cylinders tested out the same. I had good spark up to 9/16 +in. I have just recently replaced the rectifier with a voltage regulator as discussed in one of the sticky posts at the top of this forum. I will have to take boat out and see if the rectifier may have been affecting performance.