It sounds like they are mostly bonded, but I agree, it could do with a bit of extra work!
Bonded bunnies don’t do EVERYTHING together, but generally, they do choose to spend most of their time in the same area. I have a trio, and often one of them will be off doing their own thing and the other two will be hanging it out – it varies but they all sometimes want time by themselves.
Nipping to get out the way isn’t really problematic behaviour, but the grooming stand offs aren’t great. Although, as long as they resolve it between themselves without a fight, then that’s a good sign.
I think it would be good if you kept them in a smaller space for a week or so, and maybe continued with a few stress bonding car rides. It sounds like they’re mostly there, but perhaps need to just cement their bond in the new space.
The other thing is having another rabbit around can cause problems in bonded pairs. It could well be that smelling Bun is upsetting them a bit. I would be very careful about moving them all into your bedroom as it could well cause fighting between the bonded pair.