If time runs out, and the players are counting destroyed ships to determine the winner, the rules clearly state that you also count "upgrade cards equippedto those ships" so my question is, do you count equipped upgrade cards that were used and discarded during play? such as missles, torpedoes, mines, and some other cards(chewie crew) if this is answere somewhere and I missed it then I apologise

Yes you do.

Tournament rules p4

When a ship is destroyed, the owner of the ship places the corresponding Ship card into his score pile along with all Upgrade cards equipped to that ship (including any cards discarded during that game, such as missiles, bombs, etc.)

But not discarded/used upgrades on ships that are still alive at the end of the game. Those are not counted.

If time runs out, and the players are counting destroyed ships to determine the winner, the rules clearly state that you also count "upgrade cards equippedto those ships" so my question is, do you count equipped upgrade cards that were used and discarded during play? such as missles, torpedoes, mines, and some other cards(chewie crew) if this is answere somewhere and I missed it then I apologise

Yes and NO.

If an upgrade card was attached to a ship that has been destroyed then you count those point. If the "discarded" upgrade cards were used on ships that are still in play then they do not.

For example if you start the game with Major Rhymer loaded with Ion Torpedoes, Advance Proton Torpedoes, Proton Bomb, Proton Rockets, Cluster Missiles, plus a Stealth Device and Adrenaline Rush he costs 53 points with 27 points coming from upgrades. If we assume he uses ALL of those upgrades and the game ends if he is still around your opponent gets NOTHING for him but if he is destroyed they still get the full 53 points.

A ships value is determined at the start of a game and does not change after that.