Hi All,
I have a 41 9N. My PTO shaft angle hits the mower deck when raised. I tried adjusting the stop on the control slide to get the deck stopped before raising it too high and the shafts hits the very edge of the deck. Any other ideas? Of course, since it’s a 9N, the PTO must be engaged and spinning in order to raise the deck.

Can you shorten the top link without changing the mower height when it is on the ground? If you are using a PTO overrun clutch (ORC) it can change the geometry of the drive line and cause your problem. There are different styles of ORCs, some shorter than others. That might be an option.
My experiences allowed me to use my finish mower without an ORG as it had no inertia like a flywheel. My brushhog mower needed the ORC and I had to be very careful adjusting height and lifting the mower.
Also, a 9N doew not have PYO touch control like an 8N. There are accessories that you can buy that will give you touch control. Check Red Rock Manufacturing.