97 60 HP Johnson dies out

Here is the story. I was out on the lake today, picked up some weeds, the engine over heated, the alarm sounded so I shut the engine off. The engine ran on for several seconds. I cleared the weeds and fired it up. Lots of water coming out the pee tube. Now what happens is that while running along at 4000 rpm the motor starts slowing down (like it is running out of fuel). It will start to mifire and will eventually stall. I can keep it running longer by squeezing the primer bulb. Prior to it stalling the alarm sounds beep-beep-beep (not continuous like when I overheated it). I tried switching fuel tanks with no difference. I got it home on the 3 HP trolling motor. Once home I pulled the fuel line off of the outlet side of the in-line fuel filter and seemed to have no problem getting fuel to flow through using the primer bulb. The VRO tank is all but full. Is there another filter? I read in one of the forums of a fuel restriction alarm. It is mentioned in my service manual but no real details that I can find. thanks in advance