Can we assume you have tried simply turning the slow speed needle out a tad to richen it up? More to your question though, sure it could possibly be the top seal —or the lower seal. It could also be some other crankcase leak. But before you go those places, how about the carb/spark synchronization? Carb opening too soon will make it sneeze.

Well, I am assuming this engine is new to you, so you don’t know how it ran before you did the service work. This is a 1960 model, so there is no pressure tank, or pressure port tap on the intake manifold, correct? I ask only because a faulty pressure tank set up/manifold could surely make the engine run just as you have described. Have a look at the intake manifold to see if it looks to have been disturbed from original.
I would certainly check simple things first before getting in too deep. You would have seen evidence of oil spray under the flywheel while doing the ignition work if there was a problem there. I am assuming you did not disturb the upper seal components.
You mention that adjusting the low speed needle has no effect on the running quality at idle, is this correct? Like Frank says, are you sure the carb synchronization is correct? Perhaps the carb butterfly is sticky/jammed/damaged causing the throttle plate to be held open slightly at idle. What condition was the carb in when you cleaned it up? Did you inspect the low speed needle? Perhaps it is damaged/broken.
The other pesky quality about these carbs is that the low speed needle threads inside the carb are just in an aluminum sleeve that is wedged between the low speed needle packing and mixing pocket. So, if the packing nut is too loose, or the packing is missing damaged, you will go crazy trying to adjust the carb….You can turn and turn the needle, but you are not changing the adjustment…The threaded collar is just turnining inside the carb! Do you understand what I am explaining? Did you replace the packing and see the removable callar? The same thing will happen if the needle/collar threads are damaged. I wish I understood why OMC made a crazy design like this, must have been a cost savings…
Again, stick with the simple things first…The fuel pump could be funky creating an air leak into one cylinder, but usually the engine would run out of gas and keep stalling if there was a fuel pump problem. You could try pumping the fuel bulb while the engine is idling poorly to see if this helps. If pumping the fuel bulb helps, then you need to consider the fuel pump/inlet fuel lines/filter. You have tried a different tank, did you try a different fuel hose as well? Please do not disassemble that fuel pump, unless you have proved that the fuel pump is bad. Those original fuel pumps were not rebuildable, and there are no repair parts available.
A funky ignition system could certainly cause this condition, but a lean spit is usually carb/fuel system/manifold related. Although it simply can’t hurt to pull the flywheel inspection cover to be sure the points are still adjusted properly, and the flywheel isn’t rubbing on one of the leads. How did you adjust the points? Did you use Frank’s tool, or just set them to .020"? Will the spark jump a 1/4" gap?
Finally, keep in mind that the simplest of all solutions could just be one of your new spark plugs is NG! It does happen sometimes…
How about your thermostat, did you inspect/replace it? The engine won’t idle well if the thermostat is missing/stuck open.

OK, well that is good info, different carb, same bad idle….So, I guess we can rule out carb issues, and the syncro is OK….
I am assuming you checked compression and that is OK. Any signs of a crankcase leak between the two halves, or perhaps on one of the bypass covers? Again, have a close look at the intake manifold to see if someone has been messing around in there. Perhaps you have a bad reed, or messed up gasket, but I wouldn’t rip into the manifold until the other simpler choices have been looked at.