My 2000 150 EFI is running rough and I have installed new plugs, it was still running rough, and WOT would only reach 4400rpm. Today i removed 1 plug wire at a time and I was not able to see any real change when ideling at the boat house. I then removed the wires from cylinders 1-3-5 and the motor would bearly run, put them back and removed wires 2-4-6 and the motor runs almost the same as with all 6 wires on.
Running with just 2-4-6 and removing any one of the three the engine would stop, so it looks as though the 2-4-6 bank is my problum.

Plugs look the same in all cylinders, they are a nice brown. and compression is 120 in all cylinders.
I am wondering if the control module could cause this?

I switched out the coils from bank to bank to check if there may be a bad stop diode but the issue stayed at the same location.

How can I tell if I am having a trigger issue, spark control issue, or a fuel issue?

Some of you guys may have seen this before.

It is either a stator or a switch box.
Without a meter and a DVA all you can do is start reversing wires from the stator. (you can swap inner and outer)
Then if problem still exists you can swap switch box positions.

I do not have the Switchbox on my engine, I have the control module after the stator and the trigger.(a little black box)

Also... would a bad Shift interrupt switch retard the timing in bank #2 cylinders 2-4-6 ? and could it just be stuck like that?

Got a serial number?

OT100487 it is a 2000 model

Any help would be great.

With that ignition you first need to check your stator output. You can check it 2 ways 1st with resistance or 2nd and ideally with a DVA and a compatible meter.
From memory the shift interrupt switch on this motor retards timing briefly.
I expect it is your stator.

I have dropped off the boat at my dealer to have them hookup and check the stater. I will update when done.