Thanks for the clarification, everyone. I would have rolled only once for a photon for example, when the clarification seems that we roll 4, one for each damage point. I guess I missed that!
It really was a fun game. And it did get very intense during the cat and mouse and then the last decloak of the Romulan. Just a few missed protective fire rolls would have ended the game a little differently. My son is not put off at all by losing both ships, especially since he killed one of mine and trashed the other. He wants to collect a Romulan fleet so he can get his hands on some ships with heavier hulls.
I did notice after going over the rules after the game that we did the opposed crew check for Take Evasive Action! incorrectly. We used 2D6 each for the roll not 1, so that may have made a difference as well. I am not sure I like that you have an 8+ crew roll to even get to try and evade using a Take Evasive Action! SA (I would prefer automatic but with even the -1 to hit for non-seeking weapons being an opposed crew roll for the two ships), but I could see that being overused if automatic.