What does the error about missing some ship/mission data say though?
Not a lot i'm afraid its comes up with the brief message about "Fred encountered unknown ship/weapon classes when parsing the mission file. this may be due to mission data you do not have". I looked at the missions with notepad and alpha wing is supposed to be flying a new class of fighter - the GTF ferret but there is no model or table entry in the vp for it so that would all need to be recreated from scratch.
With regards to the table problems - i found them hit and miss, if you tinkered with the tbl files in any way (eg added ships/weapons from several mods into one master file) you never got the fighter laser, tactical laser or Q-W-G bomb but if you used a vanilla set from the UA vp you sometimes got lucky but there were no guarantees either way, some times you did, sometimes you didn't and sometimes the game threw a hissy fit and dumped you back at the desktop.
Other problems i have encountered are mainly limited to goals so far - a lot of missions don't have any secondary or bonus goals - not sure if this was intentional or they were due to be added as the mod neared completion. There is also mention of some UA voice files in some of the briefing dialog boxes and i can't locate them anywhere either.