[pizda]

Are you running 87 octane. Because the higher octane will create hard start conditions.
Plus fuel comapanies are changing to spring summer blend. A winter blend fuel in the spring can lead to hard start's also.
And the heat from the engine compartment can vapourize the fuel in the rails after a hot re-start.

Welcome to Ford's wonderful drivetrain.
You will always have clunking in the driveline no matter what parts are replaced. It's been engineered to do that by Ford.
Remember this is a Mustang not a Lincoln.
And the trans is assembled in Mexico. Tremec boxes are known to be very rough yet durable.
I am surprized you haven't experienced the rough cold one two shift.
Remeber the tech's at the dealer can only do so much to a car that was never really designed to be a smooth operator.