OK, so you swapped carbs completely with no real change, correct? If so, seems unlikely that you have two messed up carbs, but anything is possible. Many folks still are under the silly illusion that installing a 15hp hs jet into a 9.9 carb transforms the carb to a 15hp unit. The reed/intake theory doesn’t make a lot of sense seeing that engine idles well. You have had the manifold off and found no mouse/rats nests, so that kills that good theory as well. It surely still is possible that the exhaust is plugged up though, although I would think that the engine would blubber/run rich at WOT if the exhaust was restricted/plugged up. There are no timing marks on this engine, and I am assuming you have confirmed that the mag plate is advancing fully and the carb butterfly is opening fully. Compression is OK, and you are convinced the engine is running on two cylinders.
Anything IS possible when it comes to ignition/pack gremlins, but I am betting against a problem that is just limiting WOT RPM while the engine still runs smoothly. I am also assuming you are running the engine with the cover off which rules out any restrictions to incoming air. The engine runs smoothly at WOT, and does not bog/falter, correct?
So, I am wondering what the customer’s complaint was when he brought the engine to you. What service history can the customer provide, and when did the engine last run properly at WOT? Are you running the engine in a test tank, or on a boat? Are you using a test wheel? Is it the correct one for the engine? Are you using an accurate shop tach?
The only other simple thing I can think of is that perhaps someone replaced the propeller with one of the 12" pitch props meant for the newer 15hps.
1983 was the first year for the open megaphone 15hps, perhaps someone has messed around inside the exhaust housing.

I don’t have an 83 manual, what RPM is the proper test wheel supposed to spin up?
Looked in the 1980 manual, it says the 386537 test wheel is used, 15hp should turn up 6200RPM. BUT, it also mentions that if the engine has a reverse thrust kit, it will only turn up 4800RPM for the 15hp. I’m guessing this RPM drop is due to less exhaust getting into the test wheel’s path. Is your engine a long shaft/sailmaster/yachtwin?
I dunno, I would consider running this thing on a boat with the right prop before ripping into it anymore….

Give it the engine tuner treatment while running it also, maybe you will get lucky….

I wondered the same thing, but Joel said he was running it in the tank with a test wheel….I wonder if the newer style 9.9/15s use a different test wheel, perhaps he is using the wrong test wheel….
Joel was going to run the engine on a boat with the right prop, we will see what he reports.