If you don't want to pop a cap, why not just swab the bore with a dry patch and remove the cleanout screw and swab the bolster to breech with a pipe cleaner with alcohol if you're that concened? As for the nipple, the only lube my nipples ever get is a bit of anti-sieze on the threads.
For flinters, just a dry patch down the bore and I swab the flashhole with a pipe cleaner to make sure its open.