this is the diagram the link in question is the vertical one immediatly to the left of the finger

I don't know if I have done this right code is there but no picture

Without a picture I'm guessing, but I had a similar problem with my Twister Hawk, when the flybar came off. By a process of elimination, (read more crashes!) I found that the flybar should lead the rotor blades, although it would fit in the trail as well.

By the flat part of the upper blade, do you mean the blade ROOT, where the mounting point to the rotor head is, as the blades on any heli I have seen do not HAVE flat parts! 

Are you putting the flybar on the right way up? It is possible that the ball-joint is NOT symmetrical, and with the pivot the other way up, it would then fit. The shape of the paddles might give you a clue, the top should be curved, and the bottom either flat or hollow, depending on the paddle shape. If they are just round weights....

Before we can go any further, we need more information, and preferrably a photograph or two. (A picture paints a thousand words!) 

Hi Eric re. Photo see my last post it's the only one I have I don't have a digital camera to photograph it. yes I do mean the blade root . The problem  is that when the flybar came off it pulled the link apart i.e. stripped the thread in one of the ball link connectors so I don't know what length to make  a new one now to give the correct incidence to the upper blade. The length of the link which clips over the ball ends on the flybar and the upper blade sets the incidence of the upper blade. hope this information helps

Looking again at my Twister Hawk, the flybar is connected to the top rotor, which is otherwise free-floating, and the servos operate the bottom rotor. both  rotors are obviously driven in opposite directions by the motors.

Now - with the flybar horizontal, no matter what angle the fuz is at (within reason!), the centre part of the top rotor, and by implication the blade roots, is also horizontal, the blade angles are decided by the blade manufacture.

To set it up again by eye, get the flybar balanced up first, so it stays level, then adjust the link a half turn at a time until the rotor head on both sides of the shaft look to be at an identical angle, turning the assembly by hand in 90' steps and observing carefully until you get it as close as possible.

Before you try hovering again, ensure that the rotor shafts are not  ever so slightly bent, as that will cause the rotor to wobble, and the heli to dance all over the place!