With the assistance of another colleague we've now been able to generate a config that works for all traffic so I thought I'd come back and post the settings used. I've had it confirmed that for traffic shaping when not using a 'standard' VS type you need to use 'Rate Shaping' and not 'Bandwidth Controllers', so that was the major thing. We used a 'Performance(L4)' VS type. The Protocol Profile was left as the default 'fastL4'. In the environment is was doing testing I needed Source Address Translation (AutoMap), in a real environment this shouldn't be required so long as the return traffic routes via the BIG-IP.