Manaforte can't pay restitution sitting in jail. I doubt he can pay it anyhow if he doesn't have any more dirty money rolling in.
Biff will pardon him but I don't think that gets him off the hook for the taxes, which are astronomical by now.
Also, multiple people swept up in the investigation have hired the same law firm. That is unusual. Reading between the lines, I wouldn't be surprised if there's a benefactor trying to keep the legal fees minimized and all the suspects/witnesses reigned in, i.e. "If you want a free lawyer to keep you out of trouble, use this guy and don't get any ideas." The lawyer will have the client commit to a narrative early on so there's no conflict. Maybe I'm wrong on that, but don't be surprised if it falls out like that.
What I can't figure out is why Flynn flipped. Biff would've had his back with a pardon.