[Spoilers maybe?]

There is food in the vent in the main signal room. I've climbed all over the roof to try and find a way in but no luck so I just ignored it.

Except no I can hear flies anytime I'm in the signal room.

Is there a way into the vent? Or some way to get that rotten food down?

You can buy a hook to get in, or just bring a large box under it and place the box vertically to climb on it

Rotten food seems to reset a little when you load your game, so if you don't want to hear flies while you're working on getting it down, try saving and loading.

I would recommend using a smaller physics object to push some of the big supply crates into the signal room and try stacking them up to get a good angle on the items.