I had this problem as well. The solution is just a couple of adjustments. There is a threaded rod with two 19mm nuts, visible from the rear between the right tire and the frame. These nuts adjust how far the MMM linkages lift when the 3PH is all the way up. Turn the nuts farther onto the rod and the mid-mount parts can lift higher, but only if the MMM support arms are not contacting the stops on the frame. If they are, the threaded angle brackets that lift the support arms must be extended (unscrewed a turn or two) so the arms do not hit the stops and prevent the mechanism from lifting as far as it has to to allow the knob to go into Top position.
I disconnected the retaining rings and clevis pins completely from the threaded angle brackets, then adjusted the 19mm nuts until the knob would easily go into Top position. Then I reinstalled the angle brackets, adjusting them by trial and error until they did not quite touch the stops at full lift and both ends of the mower were equidistant from the floor.