Has anyone else had issues getting through the final mission, Vengeance? When I finally get to the point where I have to beam over to the torpedo room, Spock repeatedly tells me that there is no reason to use the transporter... I have been through it a few times, trying to follow the cluebook closely, but to no avail. Any thoughts?

It's been a long time since I played this game but there are two possible paths of this mission, a short path where you beam on the ship, discuss with a crew member and beam back on the Enterprise for the finale, and another, longer path where you beam on the ship, discuss with a crew member, investigate a bit more on the ship before beaming back on the Enterprise for the finale. The path you take depends on a dialogue choice made at some point early on in the mission. It is possible that you have selected the short path and thus don't need to go to the torpedo room. It's been a long time I played this game however so I can be wrong.

This gave me a boatload of guff.

Try using Spock's tricorder on the weapons console AFTER trying to fire a torpedo. I think that's what finally did it for me. So, Power on>Arm weapons>(Holy shoot, pirates!)>Scan console>Fire torpedos>scan console>raise shields>talk to pirates.

I just finished the game like an hour ago and this last 5 minutes drove me mad. What is even worse is that even after this mess you have the oh so fair boss fight.

I had trouble here too. It had something to do with I was clicking the red torpedo launcher instead of the panel next to it (to the left). Pretty rotten, but then I got it.