Nope, I did do one dumb thing that probably caused this.

When I removed the failed alt, I of course disconnected the batt.
As I don't like leaving my truck without the alarm on, I reconnected the batt after I was done, making sure no lose wires were grounding.
So the next day when I had the new alt, it turned out they gave me the wrong one, they matched up exactly, but the top bolt would not go through the alt.
No big deal, too late to get another one, I had some other things to do under the hood but the [censored] alarm kept setting off, so in order to turn it off you have to put the key in accessory position and hold a button for 5 seconds, I did that and it didn't turn off, like a moron I mistakenly turned it in start position - And this, of course, with no alt installed.

I heard a little click, lost all power for about a minute, I took the battery cable off and put it back on, and power was back.
But I think whatever that little popping sound was, must be the root of my problems.
Its not a fuse, I sure wish it was.