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UPDATE:

Went back to the boat today, with new fuel tank with fresh gas, new fuel line and bulb, and a can of Seafoam. Ran the engine with the new stuff, started right up and idled a bit ruff. Let it run for 20 minutes, added some extra dock lines and put the engine in gear, same thing at 2000RPM it just dies.

I then tried the plugs, pulled top plug, engine died, started right back up, pulled center plug, engine died, pulled bottom plug, ran exactly the same, no change. Would that indicate a bad plug or wire on the bottom plug?

The system is full of Seafoam as well, so I will try again in a day or two and bring some new plugs to try.

Thanks for all the feedback guys.

Paulieb

PS? I did just change the fuel filter and it looks good. I used all Honda replacements parts.

Did you check for a spark? If you have a spark at the plug wire while engine is running then you may have a bad plug or clogged carb. If you pull the #3 spark plug after shutting off the engine, and it is dry on the base this indicates a lack of fuel, if plug was not firing. If plug is wet with gas then you have a electrical problem or low compression on this cylinder. If you spray small amount of seafoam (in a safe matter with fire extinguisher handle) into the throat of bottom carb while engine is running and engine speed increases then you have a carburator problem. I am old school, do all my own mechanic work on gas and diesel engines and have done many test that are not correct procool to today's standards, if you don't feel safe doing this then please take it to a mechanic.

Derwin

Update on an old thread. I was having a similar stalling issue, It would run, (poorly) choked, but off choke it would stall at idle.
Ran poorly at 3/4 throttle to limp around. New gas, filters, different tank, inspected lines, checked plugs and wires. Cleaned carbs as best I could on the boat ad in the water, no dice, same symptoms. My nearest Honda Dealer is about 85 mile away, and I wasn't looking forward to the options of the tow, or removing the motor, or the cost. Pricing out the rebuild kits, time, and likelihood of needing more parts, I bought the carb and manifold assembly for my 2000 BF50. only came to $475 and it was here in 2 days. Swapped over the fuel lines, check valve, and air cleaner and I am back in business. All the linkages were In place, the carbs were synched, and it took about an hour.
I will likely rebuild the set I have and put it on the shelf as a spare. Should be in the water Friday!

Of course everyone here is using REC 90 non ethanol gasoline...right?
Ix

Where did you get the carb and manifold assembly for your 2000 BF50?

I looked up the parts on the Honda marine site and found part 16100-ZW4-D23ZA for the entire assembly. boats.net had it in stock and $60 under list. Free 2-day shipping. Couldn't be happier.