Why so many different shops involved in such a simple repair? As you are finding out, this is a recipe for frustration on your part as the two shops will sit back and say "not me" until any chances of a warrantable solution are long past....
First, calipers will not cause a brake pulsation.... they can sieze, they can corrode to the point where the pistons wont retract easily, they can be damaged (torn seals, broken bleeders, chipped pistons) but the reason for replacing them is always going to be readily identifiable....
The rotors, however, can make a bake pusation and they can be measured to determine this..... First, the shop can check for parallelism of the swept surfaces..... Rotor thickness is measured in four places around the circumerance close to the outer edge.... Repeat these measurements close to the inside edge and compare the readings.... Next will be the runout check.... A dial indicator is used to measure rotor runout near the outer edge of the swept area.
FWIW, Ford no longer publishes a spec on thickness variation or runout on brake rotors - modern thinking is that if a pulsation is felt, we either machine the offending rotors with an on-car lathe or we replace the rotors if insufficient material is present for machining.
From memory.... the previous spec for rotor runout on Ford light trucks and vans was 0.003".... I cannot recall the spec for parallel but I believeit was lower than the spec for runout....
Bear in mind that improper wheel installation can affect brake pulsation but, at the very least, the shop that sold and installed the rotors should step up to the plate - if for no other reason than a show of goodwill.....
And you should stop flitting from shop to shop..... Finding a tech is much like finding a family doctor.... Find one that you feel comfortable with - one that will explain anything you don't understand - one that is truthful and holds terms like honesy and integrity in high regard....