Lastly when is the best time to fire the fully charged shot? right as an opponent lands from a jump there seems to be a delay between their airdodge and shield where you can land it. Any thoughts?
This is a very good tactic that has yet to fail for me. Other than this, I commonly find myself using the Charged Beam when recovering after a smash. Usually, when someone is trying to edge-guard you, they're on the offensive. If you turn the tables around with an offensive just as powerfull, it can throw them off balance or maybe even catch them by surprise.
Ultimately, I try to keep it charged and fire it only when my opponent is at higher percents. (90% +) If they see you've been keeping your beam for that long, they'll expect you to fire it, and play abnormally defensive and make miscalculated dodge attempts / reflectors. I would tease them a little before firing.
There are two other methods I remember other people using, though I don't remember who they were.
1.) Dashing towards the opponent, letting go of the analog stick, and firing a Charged Beam.
2.) Jumping off the ledge for an edge-guard and firing the beam for an earlier KO.
Uncharged shots are good weapons to keep in mind as well, though I don't think you'll be using them as much as Missiles. Like you already stated, it can be used as a stunner (or "Tazer" as I like to call it) much like Zair.