I basically did the same thing except my volley out of stealth went for the weapons instead of shields since I wanted to make sure it couldn't hurt me after my cloak wears off. Perhaps I should start running from less than optimal fights, usually I stick out every fight because I want all the scrap.
Yeah, targeting weapons is a great idea if the enemy has low enough shields (based on your weapons load) that you can punch through them, disable weapons completely, and then do the same for the shield, while they sit there unable to shoot you, scrambling to repair.
The problem the stealth ship has is when the enemy ship has shields and weapons in abundance (those Zoltan ships are EVIL). In this case, you have to take the harder task (and almost always take damage) and knock out shields first. I loved the long beam weapons because I could drop shields for a moment and burn apart weapons and shields on most ships.
Another important thing I would always do is not fire missiles if shields were down unless weapons were still up - you will need every one of those missiles later.
