Can you just suppress them until you're done, move them to the bottom of the tree and work above them or have them as a separate part completely?
When I multibody I often create different configurations and use delete/keep body, this approach may work for you I'm not sure.
Combine.. either direct to the handle..or add a base under the brissels..ctrl select ..combine.
PLEASE do not take any offense to this, but isn't saying that you want to "merge them without them connecting with each other" a contradiction in terms? Unless I'm missing something here, in which case I'd appreciate the clarification.