Update:
Engine is warming up properly and idling at 750 rpms while in the test tank in neutral.
Compression continues to be at #135 for all four cylinders.
I disconnected the VRO from its oil source (and am mixing 50:1), checked all the idle jets and checked the carb butterflys and am still having issues. I pulled the fuel pump apart once again just to make sure all was well in there. Plenty of fuel is making it to the system. I believe this to be an electrical issue.
So, the DVA from where the powerpack connects to the ignition coils in the CDI manual is supposed to be 130V or more. All of the DVA readings on these points are right at 128V or so, although I have seen it down to 120V on all cylinders, but I beleive this to be caused by idle slowing down.
Hooked a timing light up to the motor, and all of my cylinders are triggering properly. I marked TDC for each cylinder on the flywheel and the timing light is only firing the proper cylinder at the proper time. (When hooked to cylinder 1, only 1 is triggering at TDC etc.) Resistance is correct for all timer base connections. (It is very difficult to check DVA of these connectors due to the way they connect, but i believe the voltage is there to trigger the signal properly.)
The powerpack was replaced when the boat was put up (5 years ago) and has hardly any use on it. The blue wire was shorted to ground when it was mounted, so I do not want to completely rule it out as a culprit, although unlikely. Whatever mechanic that was troubleshooting this issue in the past obviously didn't figure it out entirely.
Battery is charging well, and voltage climbs as it should under increased load. I pulled the yellow wires from the stator off of the rectifier with no change. Mis is still present.
I went to a last resort and pulled plug wires from the motor while it was running. Nice blue spark arced from the plug wire to the plug. Motor stumbled to nearly a halt when I pulled the wires from cylinders 1,3 and 4. When I pulled wire from cylinder 2, there was no change. The spark was still there, just maybe not as dark blue as the other cylinders. I also noticed that the spark plug for this cylinder was cooler to the touch than the other three plugs. I swapped the spark plug, wire and coil (one component at a time) with a different cylinder and no change. So I know all the ignition coils, spark plug wires, and plugs are all okay.
I need to check the DVA of the brown wires from the stator, but with this style connector it is difficult to get a test probe to bare wire. Is there a way to make a pin adaptor of some sort to be able to check this? The stator is the original OEM stator as far as I can tell.
Bottom line: Something is preventing the spark on cylinder 2 from firing STRONG enough to actually fire the cylinder properly, although the wire is actually firing enough to engage the timing light. At this point I believe that I have narrowed it down to the stator and/or (possibly)powerpack.
What is most likely the culprit of one CYLINDER not firing properly as opposed to an entire bank? Any suggestions here guys?