Just a thought here; and like Fleetwin says, don’t go arbitrarily replacing ignition parts on a hunch, especially MY hunch! I have never seen this on smaller OMC motors but I have on their bigger ones: How about the possibility that both cylinders are firing at the same time? The real head scratcher in your description was that the engine vibrated badly at idle BUT RAN SMOOTH WHEN YOU DISCONNECTED THE LOWER CYLINDER, AND IT WAS STILL SPARKING. Do you have a nice, open gap spark tester? Can you get it to spark at a slow enough cranking speed that you can visually verify that the two sparks are happening in an alternate manner and not at the same time? I remember watching some spark checks on V6 OMCs, where all six cylinders were firing at the same time. It sounded like some kind of space weapon….
Well, double firing ignition is surely possible, but very rare. And, the best place to begin with this theory is by doing the very basic ground/stop switch/stop button elimination tests that I spoke of. Like I said, this engine has that lovely “UFI” ignition, so replacing the powerpack is a big chore. In order to really test this theory, you need to “grid out the flywheel”, so you have a timing mark on the flywheel for #2 cylinder…Not real tough, cuz this is just a two cylinder engine, so 180 degrees across the flywheel from number one grid. Now run the engine, best done in the dark and look to see if the number two grid shows up when the timing light is connected to the bottom cylinder. Does the number one grid show up as well? But, please be ware, 99 out of 100 cases that seemed to indicate double firing are actually just the timing light reading on the number one plug wire because it is close by. And, I should have led with this, but look over the poor man’s bill from that horrible repair shop, I’m betting they replaced the UFI powerpack already, that is usually the first part “thrown” at any problem outboard with symptoms that can’t be figured out. Along with that, I repeat, that this engine requires the champion “Q” plugs, and it may misfire without them…
I’m sorry that you have ripped into this thing to the point of pulling off the head and exhaust cover. Did you see signs of water on the plugs/inside the combustion chamber or not? I’m assuming the bores look OK, even though you mentioned there are signs of overheat…How do the pistons/rings look when you peek at them through the exhaust ports? Any signs of scoring, scuffing? Once you have cleaned everything up and replaced all those gaskets, the water theory can be tested out in a different way. Remove the gearcase, now start the engine while its exhaust hsg is still in a barrel…There is no water going through the powerhead now, so it will seem to run correctly without the gearcase on if water is entering the powerhead somehow. But again, be ware, the engine will normally run differently with no gearcase on it/no load, so don’t be fooled into thinking it is running “OK” when perhaps the same symptom still exists.
And yes, usually there will be some spit back/popping when a reed is broken/damaged, but not always. On this 6hp, you can kind of “peek inside” the intake manifold with the carb off, perhaps you might see something messed up in there without pulling the manifold off. And yes, lower seals might be bad, but there are two of them down there, so seems less likely. Pulling the powerhead and removing the inner exhaust tube is quite a chore on these things, especially in salt water, so I don’t want you diving into this until all other avenues have been exhausted. And finally, there could be some sort of internal damage, like a damaged/broken piston skirt, that is causing a big leak in the crankcase, so the proper fuel air mix can not be delivered…But, this is really unlikely on such a small engine, especially if no issues are evident with the head/exhaust cover off…But, anything is possible, especially if the owner inadvertently over revved this thing severely in neutral…
I would love to see pictures of the engine along with a picture of the horrible bill this poor man just paid… Would love to hear about how the engine was running prior to this issue, and just how and when it occurred. I will do anything I can to help out, especially a poor guy that has been taken advantage of so badly.