The connection error could mean something has gone wrong with Conveyor, the part of the MakerWare toolchain that handles the connection to your bot. Go to the Services menu and select “Restart Conveyor.” If that does not work let me know and I will have a look for more solutions.
Having MakerWare on your computer will stop you being able to connect with ReplicatorG unless you stop the conveyor. MakerWare connects to your MakerBot via a service called Conveyor. Once you install MakerWare, Conveyor will run in the background and prevent other programs, like ReplicatorG, from connecting to your bot. To reconnect to ReplicatorG, you'll have to stop Conveyor. The easiest way to do this is through the Services menu in MakerWare.