With the chain in there at the back, it shouldn't need the swivel link that Luke mentioned. The chain will provide the flex as long as the 3pt frame on the cutter side can pivot on the lower bolts attaching it to the deck.
If it's sitting properly in the lower hooks of the QH, it's simply a difference in vertical measurement between the hooks of the QH and the pins. Move the hook up to suit.
The amount it's up in the top hook is about the right amount too high as if the lower pins were sitting on the top edge of the lower hooks rather than properly down in the saddle of them.