Out of the box means that the rig is still coated in assembly/long term storage grease, and that needs to be removed from the rifle, including the chamber.
Break out the CLP to clean the rig, including scrubbing the chamber with a chamber brush and CLP. Once the fouled CLP has been removed from the rig, relube the upper receiver bearing areas with fresh CLP.
If you need a source for CLP, the large spray cans of BreakfreeCLP is about the least exspensive source on the market right now (short of buying it CLP by the gallon or more from a GSA supplier). As for the barrel bore itself (not the chamber since you are going to clean that with a chamber brush and CLP), something like Sweets copper solvent does clean the the copper out for the bore fast with out a lot of scrubbing.
So to clean the upper, start with the bore and sweets to remove the copper out of the bore, run a couple of dry patches, switch over to CLP and the chamber brush to clean the chamber, and when you are pushing the fouled CLP from the chamber down the bore and out the muzzle, even when you think that the bore is dry, there is still enough CLP on the chamber and bore walls for short term storage to protect against rust. As for lubing the upper bearing areas after the entire rig has been cleaned, CLP sprayed on both the inside and outside of the entire B/C, insert the CLP wet B/C into the upper, then empty cycle the B/C a few times to migrate the CLP on the B/C to the upper receiver bearing areas (think of cleaning the rifle as just a oil change, since CLP has a cleaning agent in it that will contine to disolve any fouling that you may have missed in the cleaning process.
If you don't know how far down to pull the rig to clean it, then this should help, and semi amusing as well.
Note, CLP replaced LSA to clean and lube the AR rifles back in the 60's.
http://www.firearmstalk.com/The-M16-Cartoon-Field-Manual.html
As for the reloaded ammo, you need to run it through an ammo test gauge to make sure that it's correctly sized once fully reloaded. Not only can the case not be fully resized at resizing (bottom of the resizer not set correctly to kiss the shell holder at actual ram tension), but if you are using too much bullet crimp, then this can cause the case shoulders to slightly buckle as well. In either case, the loaded ammo will not mic correctly in a test gauge.
http://www.stu-offroad.com/firearms/reloading/casegauge/casegauge-1.htm