Thanks everyone, was indeed the mid plate that needed initialising 
I really didn't like the feel of bolts when doing it.
Anyone else who may stumble across this thread, it can be done with the engine installed as the manual doesn't specify, it's easy to do but very limited space. The Wiki on Prime had some very good steps and tips.
Things worth considering for anyone else.
There is a lot of strain applied to the bolts for the size of the thread, i felt the bolts could easily snap. Use good quality bolts and maybe a bit of lube on the threads might help to a certain degree, threading in to the flywheel there was some resistance from the threads then when you reached the mid plate it was mainly tension from the initialisation.
The instructions say to screw in until you feel resistance then apply further 360 degree then move on to the next, this doesn't work exactly to plan as you will find you will need to screw them past a certain point to clear the sump when moving on to the next.
I also bled the clutch and the manual was a little miss-leading, I was sucking through so much fluid then had massive amount of air in the system, people suggested pumping 30 times and checking fluid and some said at the end to pump further 200 or so to get peddle pressure back. I'm sure this is all good suggestions but where i was going wrong is you must not let that level go down to the bottom of the reservoir, if you do, you are sucking air back through. There was some who said you must leave the cap on then i saw a post from one of the members with a lot of experience suggest you can leave the cap off, that it made no difference. Believe it was either Old Guy, Larry or Mac and that worked a treat for me as it allowed me to keep a eye on the level.
