I use Tipton carbon fiber cleaning rods and Ultra jags (nickel plated). I don't use bore brushes much, but on the occasion I do, it's usually a Montana Extreme or Pro-Shot nylon brush (because that's what my local gun shop stocks). Again, I use them so rarely I haven't bought brushes in a decade or so.
I've been using a Tipton bore guide, but I have dreams of getting Lucas guides or Sinclair guides for all my different actions. Too much money to do that right now, though.
I use BoreTech Eliminator solvent, and cotton patches (usually Hoppe's brand, because that's what is in stock at the LGS) of the correct size for the caliber.
I do remove rifles from the stock for cleaning, and I do retorque with a torque wrench.
I'm very careful about oils on trigger parts. I use a synthetic oil which will remain viscous down to we'll below 0degF, which is well below my hunting temps, to lubricate the sear engagement. The last thing you want is for your trigger to become gunked up with solidified oils. I use a toothpick to apply just enough to create a film on the engaging surfaces.
I don't use a tool to protect the crown, but I use common sense. Don't pull brushes back through, as Mike mentioned, and be careful pulling jags back through.
I oil the outside and keep it wiped down, and I use a tiny bit of grease on the lugs to ensure smooth operation. Again, a thin, nearly invisible film of grease, not globs and turds of grease all over.
The things most people do wrong, if they're doing anything wrong, is damage the crown and leave copper in the bore.