I agree too - it may be that the shed and run is too much space for them if they haven't quite bonded yet and they therefore haven't fully sorted everything out.
Personally I would put them in an indoor cage and bring them in and sleep next to them for a couple of nights. Having them in a smaller space should accelerate the bond as they will not have the space of a shed and run to avoid each other. Clearly you will have to watch carefully to ensure that the small space does not cause distress, but usually it has the effect that they get through the humpy stage (invariably when you're trying to sleep) and start to snuggle. You could also try cheating by smearing a tiny bit of fruity baby food or squished banana on their heads to encourage them to start grooming each other... Once they're sorted in the smaller space you can move them back to the shed/run but personally I would restrict this space for a while and gradually increase it, as the move to a larger space can often kick off their territorialism again.
Good luck xx