May be chasing two different problem, if the spring was gone the IAC needed to be replaced that explains the shutting down coming back to idle. I am just guessing because I am not an expert on the fuel delivery systems, but you may have an issue with the fuel system,I know nothing on how your boat is set-up but can you run one tank all the way or half down I am guessing this will give you a list but might be worth it to fix the issue, just trying isolate the problem. It sounds like if it is a fuel delivery problem it may be past the tanks but I am not sure. That would leave the filter/ separaters, boost pump etc. I wish I could be more help.

A bad shift switch and or connection or out of adjustment shift switch can cause your motor to shut down at random. Early 496's did not have them but somewhere in 2003 If recalled correctly at certain serial # breaks Merc added the shift switch and new style bracket. Everything as far as motor, drive and transom assy goes off serial # not year. They Mercruiser will have serial # breaks when parts and part # change.

Couple of things with these Marine EFI / MPI - ECM / PCM engines is that not all running problems / codes will show up on a scan. A bad IAC and the Shift switch can be 2 of them. CDI MEDS dashboard diagnostic software will show a faulty IAC problem more so than any other software to date.

Quest,
When the spring is missing from the IAC, can this cause problems as far as being lodged somewhere? I could not find the spring while replacing the IAC.

I am not sure but it is certainly a possibility, just not sure where it would go. Maybe pull the tube off coming from the front going to the back to see if it is stuck in there.