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Had a problem with a motor (Johnson 200 HP) that ran great out of the water with a hose attached... As soon as I put it in the water and put it in gear it would stall. After I checked all of the things you mentioned, I took it to the dealer. Turned out the shift interrupt switch was bad... The switch momentary cuts out 3 of the 6 cylinders when shifting... With the bad switch, 3 of the cylinders were never firing. I thought I had a fuel problem and to this day it still blows my mind that the motor wasn't running rough... Wish I would have broken out the timing light to verify all cylinders were working...Would have save me some $$$ on repairs.
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