Reinstalling E-Tube Project should reinstall the driver (the piece of software that allows Windows to talk to the SM-BCR2), and hopefully that'll get you to the point that you can diagnose what's happening. If you can't get Windows to see the SM-BCR2, I'd pack it in and take it to a shop.
Maybe worth noting, if you can get the computer talking to the bike, it can be helpful to disconnect components to isolate the problem (eg, if you think the rear derailleur is the problem, disconnect the shifters and front derailleur). Making sure you have the current firmware on the old components may also help things get to a working state.