Are you referring to the hydraulic lift cover or the quadrant support arm which the levers are attached to?
Did you check the operation of the vertical lever (the one that makes contact with the pump control valve arm) in relation to the position of the quadrant levers, the 3-pt linkage and the position of the pump lever allowing for the fact that it is up-sidedown. It is likely that you do not have the 'dog' or 'giraffe' (look at their shape) levers fitted correctly. Did you carry out all of the adjustments to the internal linkage? Do you have access to the MF special tools?
Your tractor may or may not have Pressure Control. Remove the cap on the front of the cover and make sure that the steel tube is engaged in the port in the pump. Now that you have the plate removed from the side you can easily reach in forward and locate the pipe. Ensure that it is fitted in the pump.
Please let us know what you find.
DavidP, South Wales