In order to be able to send distance (rotation commands) to a Jaguar, you would need to use an encoder. The difference between PWM and CAN is that you can connect the encoder to a jag, and reference the encoder as a part of the jaguar object, instead of as a separate object programming-wise. It can also handle PID loops internally.
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Do you happen to know if the new Talon has both a CAN port and a PWM wire?
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Yes, it's your choice.