Let's see if I can help you with these:
1. Yes, all of the FS2 files are required to play the FS Port. The Port isn't a total conversion of the entire FS2 interface; instead, it allows you to play the FS1 campaign (and Silent Threat) in FS2 with all of the campaign-relevant media (music, command briefing animations, etc.)
2. I somewhat answered this above. The FS Port doesn't include the interface art (such as the Main Hall) from FS1. Besides the fact that this art was all meant to run at 640x480, I believe that there are table file differences between the two games that prevented an easy conversion. This may be possible at some point in the future, but for now, the FS2 interface is what you'll get.
3. Your problem with the first mission you mentioned (Out of the Dark, Into the Night) is that the Plato is supposed to be destroyed by the Shivans. I'm really impressed that you were able to kill all of the Shivan fighters (unless you cheated
); in FS1, it was very difficult to kill just one of them, even with a loadout of dual Furies, due to the fact that the ML-16 does virtually no damage to shields. The only one I was ever able to kill was the single Scorpion that stays in the area after the rest of the ships jump out. Anyway, the Plato occasionally not being destroyed by the Shivans is a known bug in the Port; since the Plato's escape pod doesn't launch until the Plato is on the brink of death, this causes the mission to glitch. You can either try to lay off the Shivans and hope they can kill it or just take it out yourself; you may get a lot of friendly fire hits, but I don't think Command cares too much, since it's supposed to die anyway.
Your second problem happens occasionally even in regular FS2; slight problems with waypoints and departure cues can cause capital ships to spin repeatedly until they manage to hit their waypoint correctly (once in a while, they never do and continue to spin indefinitely
). Since this mission happens to take place in an asteroid field, this obviously poses a problem. Usually, you can get lucky by restarting the mission once or twice. I don't remember this being a problem when I played through the Port. If it happens every time for you, there may be an issue with the build you're using.