TGS. You did not say what you shot them in.I would think, from what I have seen, that any .454 Casull from Freedom Arms would be chambered to better tolerences than what you said.
Difficult extraction could be due to too hot ammo. This sometimes comes from the factories. I once had a box of .44 Magnums from one company that was so hot, I had to pound on the extractor rod with a piece of 2x4.
You also gave the impression that the brass had stretched some. While I have never had that problem with my .44's, the .454 is loades to a much higher pressure. This may be the cause of the stretching.
I would say that if you full length resize, and then trim your brass, it should be all right for reloading. The trimming is necessary so as to get an even crimp.
If you are really worried about your out of round chambers,(I never have checked for that) I'd just contact the manufacturer and ask him what he thinks. First check with a good gunsmith, and get his opinion, preferably in writing. This will give you some leverage in dealing with the manufacturer, if it should be needed.
Hope this relieves your mind somewhat.