1. On the mission where you are salvaging a freighter, other than evading the ion storms, is there any more to it besides tractoring a cargo box and pushing it off (after beaming out all the spare parts, of course)?
No, although you are supposed to Deep Scan the cargo boxes, then transport any spares you find, not push them (the cargo boxes) off the map.
2. In the mission where you are investigating the repair dock, I can't seem to make anything happen. I enter the dock, I scan it, I've boarded it, I've tried to tractor it and drag it....nothing seems to work. What am I missing?
That mission is indeed broken. I suggest you ignore it or remove it from the Scripts File.
3. The monster that looks like a plumber's nightmare....what the heck is that?!
The Living Cage. It uses Hellbores, not Fusion Beams. The Anti-matter Eater uses Fusion Beams.
4. Does the campaign ever "end" (short of galactic conquest)...seems like my current character has been going for ages!
Yes, but the game doesn't. You finish the last mission, it says "good job" and the game goes into conquest mode.
Are you playing the Pirate campaign or the ported EAW campaign? If you look around, you might still be able to find Nuclear Wessel's suped-up Conquest Mission packs. With everything installed you can play a stock Pirate campaign, the EAW campaigns (the main one as well as the Mirak side one), the stock Conquest campaign or a custom Conquest campaign. Or you can do like I did and make up your own .mct files, choose the best missions from all sources and increase the number of missions offered to customize your own game.