First of all I like the basic outline...
This IS a cross genre campaign (my favrite kinds!) so Cannon FS2 is out the window... However to appease the masses and give a little more continuity how about stating something that teh Vasudans got dissallusioned and broke off from the GTVA. Going on their own again contact has been lost. it is assumed that either they have been wiped out by the shivans, or that they are still resisting. maybe a vasudan encounter with tense coms could be interesting "Make no attempt to follow us through the gate Terran, or well destroy you!"

Perhaps the HOL is now the majority of vasudans and once again THEY are the enemy? Whatever you want to do is fair game cause it's your vision. I'd be more critical IF it was a continuation of the main FS2 storyline.
For now , like was mentioned earlier, I would set up the tables to represent the forces to be used... Take whatever pofs that best reprsent those forces (for now) and plug them in. when you get a more appropriate model/weapon/station (whatever) then switch it out...
Ummm I noticed that you found your way to the Apocalpse forum... I'd remove that tag line in your signature about being the FS2 Apocalypse leader because USS Alexander is the leader here I believe. Also I think they are doing a TC (Total Conversion) the Homeworld campaign brought to FS2 in its entirety (is this correct guys?)... I'd change it to FS2/HW(or CAT) Crossover... BUt that's just my opinion..