My Johnson had a similar problem. It would take off great from the dock and run fine for about 1 minute, at which point it would bog and fall off plane. I would let it idle for about a minute or two and then take off again. Many days that would be the last time it would happen. Other days it would happen a couple more times. Want to know what was causing it? Ah, the suspense!
Power Packs! Not cheap, but it completely fixed the problem.