CAT6 will work fine on your desk, less fine in the real environment due to poor mechanical properties of cable and, mainly, connectors. RJ45 is a huge pain in the automotive world. There is absolutely no way it will pass any of vibration/environmental tests. Your best bet is using regular automotive wire (GXL / TXL / SXL) and hand-twist it. CAN is not picky at all. Don't forget to terminate at both ends (don't terminate at stubs). Use any appropriate automotive connector for the connections.