Thanks for the responses all, will give Joystick Gremlin another go. couldn't get vjoy to install yesterday which seems to stop Joystick Gremlin too.
The problem with doing it through DCS is that invert axis just changes my input from taking off left rudder to taking off right rudder, so the issue is that with the pedals not pressed DCS is seeing 100% pressed pedals. If i could reverse how DCS sees this i would be sorted. I even tried holding the pedal in, clicking on assign axis and then letting the pedal out to see if it would read a negative value and reverse the problem. if that makes sense.
thanks for the help.