A few days ago a buddy of mine told me that the alternator on the these vanguards only charges the battery at higher rpms (or at least not at idle).

Last night I took my family out on a stretch of the river to see the fireworks downtown. There were hundreds of kayaks out so we had to take it easy. The engine was at idle or off for the couple hours we were out there. When we loaded it back on the trailer the trim stopped working, and the battery voltage was a little low. There was enough battery that it would start. So I ran it at about 2200 rpm on the trailer and the trim would work.

If it's a 20 amp charging system then yes. The 50 amp motors charge some at idle. 2 yellow wires into voltage regulator=20a. . 4 yellow wires is a 50 amper

Looks like I have the 50 amp. Could nav lights and a 24 inche led light bar drain the battery faster than the 50 amp system can charge it at idle?
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The 50a system charges 20a at idle. Nav lights and a led bar (unless its ridiculously huge) probably won't draw much more than 20a so it would take a long time to kill the battery if those are the only accessories.

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Also, from time to time, the charge can get lower and lower depending on usage. Chances are yours was low when you went out. It's best to keep a battery tender on it and you won't ever have a problem.

So there is more to the story. I took the kids water skiing yesterday. When we left the mud boat was at the dock with the trim all the way up. When we came back the trim was all the way down. I figured it must be leaking. So I hit the switch to raise it back up. As I was walking away I heard the trim turn on and go down a few inches then stop. Then a minute later it went all the way down. So I raised it back up and started to walk away again when the trim motor turn on again, but this time it was trying to go up. Only way to stop it was to disconnect the battery.

I looked in the football to see if there were any obvious shorts. Everything looked fine. Any ideas what’s going on?

Sounds like a bad switch and the culprit draining your battery.