Hi,
Compression seems acceptable.
Are you running fresh NGK DR7EA
spark plugs?
I don't know this particular model but I'm very familiar with the Keihin carburetors on several Honda models.
I see from the parts list this outboard has a Service Enrichment system instead of a conventional choke. Please correct me if that's wrong.
If you have an SE valve in the #1 (top) carburetor then I suspect that there may be an enrichment issue with the SE valve or with the power that leans the system out after warm up.
The SE system is always defaulted to rich when the engine is off.
After start up, a dedicated mag coil under the flywheel starts supplying voltage to the SE valve.
After about 3 minutes run time, the electrical heater coil inside the SE valve causes a wax pellet to melt. The melting wax expands and pushes the enrichment pintle valve down against spring pressure and closes off the enrichment passage leaning out the air/fuel mix. The system stays in this configuration until the engine is stopped.
Things that can go wrong:
The coil under the flywheel doesn't supply voltage to the SE valve after the engine starts.
The SE valve heater fails to melt the wax pellet and the needle valve doesn't extend.
The SE needle valve gets scratched and won't seal.
Or, the seat gets worn and won't seal (very rare in my opinion...I've never seen that happen).
You can unplug the SE valve and check that the coil under the flywheel produces voltage after start up. If not, check the continuity of the coil and wires at the connector. I don't have resistance value for that coil. Sorry.
You can remove the SE valve and apply 12volts to the SE valve connector and observe that it fully extends after 2 or three minutes. Be careful not to get burned doing this as the SE valve gets very hot!
I Don't have the 40hp shop manual but my 20hp manual says Positive to brown/white and Negative to black/green.
It also lists resistance as 15.8 to 24.2 ohms.
Based on what you said the symptoms are, that's my best guess as to what to check from my not so easy chair.
But, if the enrichment system checks out good, I would then suspect a possible timing or valve adjustment issue even though the compression numbers look "ok".
Good luck.