This is kinda long winded but you kinda need the full turn of events to understand whats going on here....Please Help

Well heres the story....about a month ago I had a broken water pump base. I had it fixed and all the seals redone in my lower unit. The next week after I had it done I went out to Bastrop and the boat did fine all day until I was ready to put it on the trailer, the overheat alarm went off after I idled around the ramp, no grass no nothing. The alarm would still go off when I turn the key to the on position as to let me know not to crank it and that it was still hot.< (This is impotant for what happened today.) I then took the boat back to my mechanic turns out the starboard side thermostat was froze up so I had both replaced. The next weekend I went to Travis no problems what so ever boat ran great all day. Yesterday I went to Georgetown and the same thing...boat did fine all day. Now on to today. I fished Decker today and when running about 1/4 mile the other side at about 3/4 throttle the alarm goes off. I shut the boat down immediately then turned the key to the on position....no alarm (what the heck?). I lift the motor check for obstuructions, nothing. I lower the motor back down crank her up and idle around the about 10 mins....no alarm. I decide to head for the ramp....the same place I was coming from when the alarm sounded before. It went off again on this run and the same thing happened....after shutting down and turning the key to on there was no more alarm like there has been in past times it has gone off. I idle around in a cove for about 15min and no more alarm I fish a bit more then put her on the trailer. I just can figure out why this alarm would go off and then not stay on...if it is truly over heating it would take way more than a few seconds before it cooled. Anybody have any idea or suggestions on what could be going on here?
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Sounds like you need to replace the poppet assembly.

Don't keep running it. If the horn goes off, then you turn the key back on, then no horn, I would lean toward the module itself. But you need someone to check the cooling systems. You're playing with fire if you keep running it like that, because if it really is overheating, you may have already damaged it, and the damage just hasn't shown itself yet!

I'm from the old school myself.. If that motor is overheating u can definately feel it on the motor. It should be warm to the touch upper and lower on the side of the motor, and that's normal. If it feels hot in one spot, cool in others u got some obstruction in your water channels that could be causing a overheating issue. The bad part is, on one cylinder. I sure wouldn't be running it on the lake if anything even close to that nature is taking place. But here is something else to think about, who said that the sensor is working properly either? It could be intermittingly giving the wrong readings causing the alarm to go off too. Just a thought, sounds like the parts and components u replaced should have fixed it.

Its the poppet valve. Easy fix and parts are cheap.

Can someone explain what it is and where on the motor it is located? I would like to do this myself to avoid another trip to the mechanic

Starboard side, low, below the power packs. You will see a raised round cap with a small hole at the bottom. Best to get your motors model and ser# and go to: http://www.mercurypartsexpress.com/us/index.html