Control System Problem Help?

[rogeringalsbe]

Good afternoon,
We are a rookie team and having a couple of problems. We first uploaded the update to our driver station prior to performing initial control system testing (mistake 1). Then we couldn't get the driver station to talk with the CRIO. We thought perhaps there was a way to revert the driver station to Out of Box revision. We couldn't find a way to do that (mistake 2) so we took someones advice to someone else on the forum and reformatted the CRIO (mistake 3) and then updated it with latest firmware. Then we could get the CRIO to provide battery data to the driver station but we still have flashing yellow lights on our jaguar controllers. We have triple checked the wiring, replaced one of the controllers to see if the "new" one worked (it didn't so we switched back), installed the 6v jumper on the digital sidecar and checked for proper voltage output (we got it). We thought maybe the CRIO's default program was wiped so we tried to install a new program (now the driver station doesn't see the battery anymore get a "No Code" fault code). The digital sidecar is getting the correct input for robot online or offline (indicated by the light) but we get no signal to the jaguars.
Could it be that we wiped the default CRIO program and now it doesn't know to tell the jaguars to turn on?
Could there be a problem with the digital module on the CRIO?
Any ideas would be greatly appreciated.

Thanks!