[Joe Ross]

Can an Arduino even run Java?

The problem is that the WPILibJ libraries are tied to the cRIO hardware. For every cRIO hardware call, you would need to replace it with a call to the equivalent feature in your new platform. For example, in the PWM class, rather then calling the FPGA function to generate a PWM signal, you'd need to replace it with the generate PWM command on the Arduino. When you've done this will all the source, I expect that there won't be any calls left to com.sun.*, as well as edu.wpi.first.wpilibj.fpga.*. In addition, the communication protocol is handled by a compiled library which edu.wpi.first.wpilibj.communication.* references. You'd need to re-implement all of that also, based on reverse engineering the communication protocol. There are probably other things you need to do as well.

The Jaguar CAN protocol specs are included in the Jaguar SDK. You will need to program the jaguars to the stock firmware, rather then the FRC firmware. This is because the FRC firmware runs in a "trusted" mode for which the protocol is not released.