I had a similar problem on a 3000 twenty. The lift arms would not lift the backhoe high enough to get the pins in. I adjusted the position linkage and in minutes the problem was solved. Attached to your left lift arm, when viewed from the rear, there should be a threaded adjuster with two jam nuts. Loosen one and tighten the other in very small increments each time lowering the rock shaft and carefully bringing it up to max to make sure the lift arms are not hitting anything. It has been awhile since I made the adjustment but I believe I turned the nuts clockwise to increase lift height. If not just go the other way and make sure both jam nuts are tight when you are done. A small increase in lift arm height will make a big difference to the height your PHD will go to.
Since this is a new machine the dealer would probably make the adjustment at no charge but because it is a quick fix I thought I'd post this.
Be careful and congrats on the new machine.
Regards,
Tom