Just some ideas and comments on your project here:
First before asking for mission builders, you might want to present a clear picture of your mod's basic premise. A website would definitely go a long way to presenting and advertising your mod.
I'm not really sure where your story is at or whether you have gone away from the merc premise. I think the merc premise could work, but it would need to involve a large scale merc corporation ala Blackwater on even larger scale.
Using old Kilrathi era warships (probably Caernarvons, even older frigates and beefed up transports primarily) bought from Confed, doing jobs from various large and small-scale governments and corporations including various escort and militia duties. I would imagine the Border Worlds would be a good place for business given the Kilrathi raiding parties and relatively poor territory (outsourcing militia work might be cheaper than maintaining their own).
Also, regarding maintaining these ships (at least from the crew perspective), didn't the Tarawa have a crew of 300? With the high decree of automation that one would expect for this time frame, a destroyer could be probably function on a crew of 150 or less, which wouldn't be a big deal if the mercenary corporation is large enough or part of a larger mercantile corporation.