I personally would stick with the original plan. It's different if you've got a mom and kits travelling together, and even bad things can happen as I've experienced first hand. Animals get upset, they start jumping, and babies/roomies end up mangled or dead. It would even be different if these guys had been together for years or even several months. They haven't. They have been forced together without a proper introduction other than just the stress of removing them from one place to the next, and now they may be facing a 16 or even 18 hour drive or more depending on where they are going, shoved into a cage with a relative stranger. The last thing you need is to be hauling butt down the interstate and have a fight break out behind you. We all know it takes seconds to do some serious damage. Maybe not life threatening, but it only takes one good bite to gouge out an eye. If they were getting along before you transported them, odds are they will be fine again when they get to their destination.
Stick with the single carriers.