I can't help with the LED trick, Iv'e always had access to a scan tool. But I have had a few MEFI's that wouldn't connect with the normal connector and would have to use the connector for a merc outboard that has separate battery clips on it. The times I ran into that everything else worked fine in the ECM. So I didn’t look into it anymore.
But to be honest, Iv'e found over the years that codes are the smallest part of scanning a engine. Over 80% of the time all a scan tool does is quickly rule out a bunch of things that might be causing the problem.
Also, I can't help with the MPH vs RPM. Most of my time in the boat business has been spent with twin or triple engine go fast or cruisers.
Once you find out how much $$$$ it's going to cost to replace/repair your engine. You will want to know why it failed in the first place. Otherwise it will probably happen again. I don’t know if you are going to attempt this diagnosis/repair your self or have a shop do it. But here are a few of the failure causes I’ve seen.
1. Overheating, a experienced 496 mechanic will be able to see this during disassembly.
2. Part failure, (cracked valve spring, connecting rod bolt, ect.) easy to find during tear down but doesn’t fit your symptoms.
3. Abuse, lack of maintenance like oil changes, exhaust manifolds (water intrusion) —- propping/gear ratio (this one is common, the boat is propped right for normal usage but then I find out the customer is loading the boat with 15 people and dragging a tube around all day causing the engine to be severely overloaded) some of these can be harder to find without good input from the customer.
4. Fuel injectors, this one is becoming more common. Stop to think about injectors. At the age of this boat, most carb engines would have had the carb rebuild/cleaned once or twice already. Carbs are a mechanical device that can wear or plug up. Injectors are mechanical/electrical so two possible modes of failure and the passages are much smaller so easier to plug. I highly recommend they be sent out to a good rebuilder. One that mostly does marine injectors because even though they are same as auto injectors, the failures can be different. This is best done early in the diagnosis because a good shop can give you help on what cylinders might have been damaged by the injectors. Also this time of year all the good shops will be backed up. And this applies to boat repair shops also. If you call five shops and four of them are backed up two weeks but one of them get you tomorrow. That one is either lying to you or they’re just so bad nobody else trusts them. And beware of shops/people who recommend “on engine cleaning” because this is more likely to make things worse than better.
5. Worn out, not common in my area or on property powered hulls but maybe you have 1000 hours on the engine?
Hope this helps.