Your stock rattling on the buffer tube is normal so don't worry about that, most AR's with non milspec buffer tubes do this, it's just another downside to mass production. Unless you go with an aftermarket set up from Magpul, LMT, or Vltor that utilize milspec buffer tubes and tighter tolerances you'll just have to live it.
As for the charging handle, you wouldn't happen to have a Badger Ordnance tactical latch would you? I've seen similar problems to what you're describing from people that have them and it comes from using a one handed charging motion. When you pull the CH, it's designed to go straight back where there's the least amount of resistance and metal on metal contact. When using a tac latch, pulling the CH causes it to rub against the upper receiver's raceway and cause what could be called "excessive wear," I'm not sure if you do this but I was just throwing it out there.