[MattG_3165]

The first things that come to mind:

Don't build your cable to the manufacturer's spec, i.e. using flat wire and putting the CAN terminator in the DB9. This may work for short cables, but it opens up lots of noise/crosstalk potential with CAN and RS232 traffic on parallel pairs of wires. Use shielded twisted pair instead, and put your CAN terminator at the Jaguar end of the cable.

I can't determine from your post if you intend to use cable with an integral braided shield (STP), or if you intend to slip a separate braided shield over your otherwise unshielded cable. I recommend the former.

If you use shielded wire, you have some connection choices: the DB9 connector shell on the cRIO which is connected internally to cRIO chassis ground and should have true ground potential, or the robot chassis, which is not necessarily true ground potential, as your electrical system should be isolated from the robot chassis. Since the cRIO is normally isolated from the robot chassis (required by the rules), connecting the shield to both the cRIO and the chassis should be avoided. The signal ground (pin 5) is sourced from the cRIO. Since you already have a cRIO-sourced ground running through your RS232 cable, it makes sense to ground the shield to the same place, ie. the cRIO. This might be tough with an RJ-12 to DB9 adapter though, as these are usually plastic.

Maybe the easiest way to go about this would be to re-purpose an existing serial cable. They're usually already shielded and have the shield connected to the DB9 shell at one end. Just cut off the other end and attach a CAN terminator and RJ-12 connector, and you're good to go. Shorter is also better in this business - don't make your cable longer than necessary.