Hi mowerguy,
Well, I've never worked on one either but I've got some ideas that might interest you.
The ignition firing and timing is done via presets "baked in" to the CDI ignition control module. It's non-adjustable as far as I know.
The CDI receives rpm input from the Pulser Coil module located under the camshaft drive pulley. See item 10 in the link below.
It's important that the pulser is properly bolted down and the wire connector is securely locked but, other than that, not much to it.
It's my opinion that the slight misfire/stumble you're sensing is more likely to be attributable to something other than ignition timing.
The rpm difference that you see with the top carb might be an indication that there's a slight restriction in the idle/low speed circuit. I don't know. But it is something to consider.
I have a very strict regimen when cleaning the Keihin carburetors because they can be so difficult to clear sometimes.
While I think I might connect a quality vacuum gauge and watch for the needle to bounce when you feel the issue, it might actually be much simpler than a valve train concern.
I mean, since it's a new purchase for you, it might make sense to do some de-carbon treatments right off the bat to see if things get better.
If the outboard did a bunch of trolling before you got it, there could be carbon buildup.
Carbon will absorb some fuel mixture and maybe...just maybe...that could be affecting cylinder firing.
At any rate, many people have seen marked improvements from running big doses of Sea Foam or other products in the fuel to help clean the combustion chambers.
While I would certainly not argue with checking/adjusting the valves, de-carbonizing treatments could be a good thing to try.
Your call.
Good luck.
