Hmm, my shop manual on CD says that the Continuous beep from the Guardian system could mean any of:
Cooling system problem
Oil level is critically low
Oil pump failure
Engine overspeed
Sensor out of range
But in all cases it says that the Guardian system will limit rpm to anywhere from a "fast idle" to "rev limit kicks in" (depending on the cause). In no case does it say that any of these conditions will make the Guardian system prevent the motor from cranking or starting.
Kinda vague here I know, but it sounds like maybe you have one of the listed issues (causing the alarm), and either: that then caused a more serious issue, OR also you have some coincidental, unrelated issue.
I'd start with trying to figure out if we can easily determine what triggered the alarm, maybe that can lead to whatever your other issue is...
Had any issues with the cooling? Impeller replaced regularly?
Oil level in reservoir OK? Ever change out the oil reservoir filter?
Another Q: did you do any rewiring while swapping batteries in and out? Any chance you made a dead short (or installed battery backwards!) for a moment, knocking out a fuse or fusible link on the outboard? Guess this could lead to a "sensor out of range" issue, eh? As well as explain no ignition power to your gages and such.
But you say you have no power to ANYTHING, is that correct? Did you try removing and re-installing the batteries...maybe the terminals aren't as clean as you thought? Or maybe the crimps on the lugs on the cables have loosened somehow? Or maybe you've also knocked out your main fusepanel feed fuse, too?