Re: Johnson 1995 48hp revs fine when not in gear, but in gear wont go full throttle !
I would shoot a litttle premix fuel in the top carb and see if the engine surges some. If it does then it is a fuel issue.
Pull the fuel pump line from the pump to the carb off and with the lanyard/kill switch in the off position crank the motor with the hose in an old pop bottle. You should get strong steady surges of fuel from that line. If you don't suspect the fuel pump. BE CAREFUL you can get splashed pretty badly if you don't keep the line way down in the bottle. Stop cranking the instant you see good stong surges.
Another way to test the fuel pump, if the boat is in the water, is to take it out and try to run up to speed, when it falls off pump the ball and if it surges back suspect the fuel pump. If the fuel pump tests show the pump is OK, I think pulling the carbs for a cleaning or rebuild is a good next step.
Also check the fuel filter it could be clogged and not letting sufficient fuel flow.
You could also have an issue with the tank or hose, try a portable tank and different hose before you pull anything off the motor.