[jhersh]

If you weren't using CAN last year, then you weren't using the Jaguar's PID. That is the only interface to enable the internal controller.

If you want to run the PID controller on the cRIO, that's fine. I'm surprised you wrote your own given the very capable implementations provided for you.

There is no way for you to replace the PID algorithm in the Jaguar. You may either use it as is via CAN, or you may ignore it and run any other PID implementation on the cRIO.