No such thing as a stupid question...
No, you will not lose any program in the PCM if the battery is disconnected.
Not sure how to make the "gauges" really work - and I have my own doubts about the volt meter really working anyway. My battery light flickered on and off for a couple months while Ford replaced the battery, then the alternator (which finally cured the problem) - but the volt meter stayed right at 50% all the time. Replace the whole thing with the Autometer Lunar cluster...I believe those are real gauges.
I know what you mean about the volt gauge being questionable. I mean, I turn the ignition on, and start the engine, and my volt gauge only moves slightly. You'd think if it's not real, or not accurate, that Ford must really have been cheap.. I mean you can buy a friggen functional Autometer volt gauge for 20 something bucks.. you wouldn't think Ford would skip something like that.. but hey.. it's Ford.