Prob #1: I installed MA3, set it as default SS, and then entered a keycode. All was well, until I realized tonight that my machine, although unattended, had not gone to sleep as usual. The monitor had shut down, but the MA3 music ,and I presume the SS itself, was still running, and the machine was running with all lights blazing.

I thought that was "normal behavior" for MA. I am sure that I have a Vista Ultimate 32 system with MA2.6 that continues to play the "bubble sound" after the monitor is turned off (by the automatic power settings) - at least as long as the computer doesn't go into "standby" or "hibernate". [Perhaps your settings are different, though].
I'll have to test that on MA3 when I get a chance. Or, Jim can tell us what the sound is supposed to do under various conditions.
Prob#3: ... When I did this I got 3 entries in the SS Settings dropdown list: MA3 and MA2 + Time, and 1 called "PSerenescreen Marine Aquarium 3." ...

Just after I installed MA3 (Installer version) on an XP system, and asked the installer to make MA3 my default screensaver, I am certain that I saw TWO entries in the Screensaver list for MarineAquarium3. Both identical names, I believe. But after I did "something" (clicked on one?), one of them went away. Perhaps that's a clue. I would guess that it's some "artifact" of the installer that corrects itself - but perhaps it needs to be kept on the list of reported installer bugs?