WELL....
My problems didn't stop from the last post... Far from being trouble free.
After doing the dizzy turny wire swappy thing that made the engine run like BUTTER, it ran good the next day too. The day after that, it ran good again, so I decided to finally take the boat out for a test run and take on some fuel. Well, I cranked up the engine, ready to head out for a test, and it went back to square one.
Damn, I was PISSED. However, I realized that if I give it some revs to keep it running for 30 seconds or so that was the required amount of time to get it to push the IAC full open. With the IAC almost full open it would stay idling without stalling and let me go in and out of gear. The engine sounded like crap and was clearly misfiring but I decided to go ahead and see what would happen if I got on the throttle. So I took the boat out, and as soon as I got past 5% throttle the engine would run excellent, no misfiring. Back to idle and it would miss.
Ok, whatever, it runs good on plane, and fall was around the corner, so I decided that the engine should get me from Annapolis all the way up to Canada, and then I would mess with the idling issue when I got the boat home. First day, did about 80 miles uneventfully. Next day I wanted to do even more but the sea was very rough past Cape May so I had to take the ICW. Then I ran into the Dorsett Avenue drawbridge in Ventnor city that was broken and wouldn't open so I ended up doing about 95 miles that day. The next day I did some shopping in Atlantic city as I had lost my barbecue in the Delaware bay, the chop caused the barbecue to rip out of its post on the swim platform. Waited for low tide, removed everything from the radar arch, and managed to squeeze under the bridge with about an inch of clearance. Whew!
Did only 40 miles or so that day, and basically got up to Barnegat bay late in the evening. The next two days I was just moored waiting for good weather, and then with somewhat tolerable ocean conditions, I headed out to make the final run to NYC. I was a third of the way there and then I heard a loud ROD KNOCK

! Only thing is that it was coming from the STARBOARD engine, that never gave me any issues. Limped back to the place I moored at on one engine, and had the boat hauled out. Checked the compression and it was kinda missing in a few cylinders. I rented a uhaul van, took both engines out and headed back home to Canada with them. So now I have two bad engines

.
I do have to mention that I did the cylinder heads on the starboard engine (the one that was problem free), since a couple of cylinders were a little low on compression and these engines are known for dropping/sticking valves. Had the seats, guides, and seals done on them. Also converted to adjustable rockers so I can manually set the preload.
Well, I tore the engine apart a couple of weeks ago, and the cylinders and bottom end looked absolutely pristine. Not a scratch on any journal or bearing. So I doubt that the knocking noise would come from the bottom end. The pistons and cylinder walls are in good shape too. The only place I could loose compression is through the heads, so I took those back to the machine shop. Got a call from them and they said the thing got extremely hot/lean and warped the seats and guides and they wonder how it even ran at all.
What a head scratcher. It never misfired or anything, but what both engines did was blow a fair bit of steam from the exhaust. Neither overheated, but the exhaust water did get quite warm. I did go through the entire cooling system, and all the pickups, strainers, coolers, heat exchangers were clear. I also installed new exhaust manifolds and elbows. Even at idle, the water discharge from the exhaust was like a fire hydrant, so I assumed the steam was normal.
Well, maybe it wasnt and was telling me something was wrong. I don't know. I also don't know where the heck I am going with this post, but anyways, I have the port engine home right now on a pallet, and I will try start it outside of the boat and see what it does.