FOR THE LOVE OF GOD, DO NOT DO THIS, I REPEAT, DON'T DO THIS. This will irreparably brick your game and make several missions unplayable as well as the campaign. You get the ACCURSED "check starfarer.log" mission description bug which will makes the missions that have this description unplayable as well as the campaign. Until somebody actually digs through the code and adapts this mess into something that doesn't require CONCORD to function, do not use this (or any of Sutopia's) mods.
Which missions, in-campaign or otherwise? Maybe it's a peculiarity my own (heavily-customized) mod setup, but I haven't encountered the bugs that you have described.
As in, I've recently completed several campaign playthroughs; mainly, the Galatia Academy mission chain (re: to unlock the Gates).
That said, I haven't gotten around to
finishing the
other 0.96 mission chains as-of-yet (which
could very well be bugged to hell).
EDIT: If you are referring to the 'Missions' menu being unplayable, it is most likely because the custom loadouts still contain references to Concord-related hullmods that no longer exist; same for any campaign saves that even had Concord loaded even ONCE.