So, I've been thinking about the best way to play as Mush on a good ship.
I think initially, your best bet is if one of the Mush finds is acceptable to go home early by being "obvious Mush" and doing everything in their power to delay the crew being productive during the first day or two. To make themselves a target. This should be done immediately before day change - take down a camera, spore someone, partner spores them, day changes, spore them again, and partner then takes anonymush.
You've now changed the situation from "2 secret mush" to "one obvious mush and two secret mush" which seems like an obvious improvement, especially since you've converted a target of your choice, undoubtedly some essential to the functioning of the ship.
The partner, with his remaining AP, should then try to do as much damage as possible before (inevitably) getting killed. Aim to waste as much human AP as possible that would otherwise be going to something important, and doing it this early means you might have done NOTHING to help the ship. Getting armor and taking hard-boiled is recommended. Alternately, if he has pilot, take down cameras and head out in a patrol ship or in the pasiphae!
The ship is now down one human, a bunch of AP and maybe some important equipment.
The next day, do it again. On day change, rush-convert someone. Even if one of you gets outed somehow, you can go on the same rampage and waste the ship's valuable AP, and you still end the day with two mush!
At this point, you've probably been able to cripple the ship's leadership with blatantly converting the most active and useful people to your side, and they can probably organize things to feed the rest of the ship to your conversions.