Transporting into a new BW system from a shared dev system

We are currently in the process of setting up a new BW system in the same landscape as our existing one where both boxes will share the same dev system. Our existing one is used by many different applications and has tonnes of shared objects on it. Our new box will only be used for SEM-BCS and thus does not need everything else that the other box contains. Since many objects are dependant on others (attributes and such) I am finding it hard to get transports into the new system. There always seems to be something missing even when I try to just move a single object. I also seem to be having troubles with InfoObject Catalogs where they cannot be moved if the InfoObjects are not there and the InfoObjects a cannot be moved with the Catalogs not there. This is all starting to give me a serious headache.

Has anyone delt with transporting to separate systems from a common development system? What is the best approach to this to ensure we only move what we need to the new system?