I have the virus now, but Mars needs to become more Earth-like before I can attack the fortress. For 5 months now, Mars has been 62% terraformed and the number has not budged at all. Water has dropped to 4 from 7. I've the upgraded water tank, and the only way to get more water is to capture a shaman which I cannot because the beasties are now confined to their fortress. My rockets are doing too good of a job stopping their advances....

Well, unless you let the BM take back a few territories whenver they manage to get pass your rocket defenses you're pretty much at a dead end.

An alternative would be to edit a save game to turn over some of your territories to the BM, missions should start spawning after loading the modified save.

You could also create a custom mod to remove the shaman interrogation prerequisite from the research topics you have locked by it.

Unfortunately I'm not a programmer so I dont know how to make a mod to remove the shaman prerogative.