I NEVER experienced wheel hop with my tuned 2010 MKS and most certainly never a thud at the shift point. I suppose the wheel hop could be due to your tires, tire pressure or the surface that you were launching on. Otherwise, I wonder about worn suspension components.
The thud at the shift would concern me. Shodded makes a good point about fresh fluids. You might want to have them back off the shift pressure a bit, if fresh fluids do not cure it.