Disconnect the cylinders from the frame and lower the top's hydraulics so the cylinders are retracted, do the cyls retract all the way or close to it?
with the cyl disconnected can you manually lower the top without binding to a position you feel is acceptable? ( be careful it might get heavy and be sure the cyls are out of the way of any moving frame parts or top material)
is it possibly that the top never was intended to lower to as flush as you expect it to?
