Okay, looks like that fixed it! There were dozen's of instances formed from two different texts with // . After removing, the level loaded correctly.
Thanks a great deal for all the help, Battuta, Karajorma and FUBAR. Let's see how good I can make these missions - Learned a lot lately and want to apply it as much as i can

EDIT:
Ookay, while we are at it, a new problem has arrived. Mission 1 works great now, but now Mission 4 is having a different problem. I'm hoping we can take a look at it!
[Removed link]
Mission CTD's on load sometimes, and else it reports various problems with Special HP/Special Shield and other settings. Even after removing these entries through Notepad, it persisted.
Below, one of such warnings.
Error: C:\Program Files (x86)\GOG.com\Freespace 2\data\missions\Classified_Mission4_Gather.fs2(line 171:
Error: Required token = [#Wings] or [$Name:], found [+Special Hitpoints: 1050] .
File: PARSELO.CPP
Line: 670
Call stack:
------------------------------------------------------------------
------------------------------------------------------------------
It worked fine two days ago when I last tested it, and I haven't changed anything to the mission itself till now. Very strange and random.
Hope to hear more soon!