The easiest way for this effect is to just place in the file, and obviously launch entirely from the first person view or inside the flight deck, and the effect is created due to seeing the damage on the orbiter once past OMS 2 for Payload opening as it would of happened on that mission.
But as a way of giving the Launch scenario a more dynamic feel on occasion into a launch it would be a tad more interesting if there was a automated command given to load in another MGAtlantis DSS file with those new changes to it.
I'm not knowledgable in the know how on how to make this possible, if anyone is interested, I can upload this modified shuttle texture. I even typed up a different name on it.
The highest orbit during that historic mission was 156. The technical stuff is different from some web pages than the actual film. I think the film said four burns were done for begining of the mission.