I'm confused...how bad did your car overheat on the dyno? Did they keep doing WOT runs back to back or turn the fans off? Has your car overheated before to make you change the thermostat? What makes you think the head gasket is bad?
When I took my car to McNews: First Ray did some easy pulls through the RPM band to check the base tune (which was pretty good). Then made some tweaks, loaded new tune (that took 5-10 mins with the XCAL2). Then 1 WOT run. Made some tweaks then loaded new tune (another 5-10 mins to load). Then 1 WOT run. Made some final tweaks and loaded the final tune (another 5-10 mins to load). Then the final dyno pull for numbers. Basically there was always cool down periods between runs while Ray tweaked the tune and then loaded it. Granted loading a tune with the XCAL3 is quicker but there is still cool down time.
What da heck was being done on your dyno runs? The Duratec cooling system is very efficient I never once had any issues with overheating even at ambient temps close to 100* F and sitting in traffic.
2010 Ford Escape 3.0 V6
2004 F350 6.8L V10
1986 XR4Ti 2.3L Turbo
2007 ST ; formally bewst'd - R.I.P