For the knee, another thing to do is just glue in a tiny piece of padding on the inside, just enough to soften the buffer between your knee and the armor.
As for the boots yes...your days of being "death star shiny" are ending and you can expect some wear and tear on the boots (especially the ankles, due to rubbing), and the armor, in time.
SOME of the fit issues will resolve themselves as you troop more often, your body will adapt and get used to certain things. Other things, you need to adjust. It may take some time/troops to really figure it out. There will be plenty of TKs (in and out of costume) at the RCCC, if you can make that.