SIR Isaac mentioned this happening to carbon fiber hoods while they were in their boxes, and then not fitting correctly when they were installed because the box had mis-shapen them.
he said to just leave it out in the sun for a while and then try installing it again.
what skirts do you have? they might not be mis-shapen, they might just have bad fitiment. if your shop didnt modify them at all and they had poor fitiment, then heating the glass wont do anything. you would have to take them back to the body shop and have them modify them until they fit right.