Thanks Simon,
I've forgone the attempt to supplement the factory control and gone full control by the Link, It's all working fine now under the conditions I have set, however I now have a check engine light come up with a TCC lockup circuit error that will be fixed once I get my 5.6ohm resistor to simulate the solenoid.
One question though, is it possible to slowly ramp in the PWM up to a fixed figure? I was thinking ramping in over a one second period or less, making tcc lockup a fraction less harsh.