Just thought Id post here the final results and what worked.
First off, Im running the OS supplied header and pipe (the Hatori #900 2C140 pipe) and was using a 16x12 APC prop.
Today I cut 8mm from the header pipe to get a shorter effective header length and changed to a 17x12APC prop.
Runs fantastically, 7800rpm flat out and an idle of just over 2000rpm (a tad fast I know but until its broken in properly it'll do) I can let it idle for 30 or more secs and go to full throttle with no hestitation or rough running, I can slam the throttle open or closed and no problems.
Seems the pipe was too long for the prop I had and not enough load on it with the smaller prop for it to get on the pipe properly. After flying it I may find I need to shorten the pipe some more to adjust for the unloading of the prop in flight.
The info to get it going came from another local guy who's had exactly the problems I was having.