First things first- THE BUILD.
When building seal the gas tube into the gas block(permatex gasket sealer or blue loctite will work). Make sure the gas tube is right side up and pinned properly. Remove the rear set screw of the gas block. Look down through the hole and make sure the gas tube is not obstructing the port in the top of the gas block. If it is drill it out, most will allow a 9/64" bit without damaging the threads at the set screw. When installing the gas block on the barrel use the same sealer to cut down on gas leaks. Place the rear set screw hole over the dimple in the barrel. Tighten the front then install the rear set screw and tighten it. Careful with the loctite the screws are very small and allen wrenches strip easily.
Continue the build. When finished from the rear run a patch with solvent on it through the bore to remove excess oil and any dirt or grit that may have accumulated in the bore during transit and building. Run a dry patch through to remove any excess solvent or oil. Next clean the chamber AFTER cleaning the bore to remove any junk that was splattered into it when cleaning the bore. A 28ga bore mop spun by a drill works well. You can use JB or Iosso bore paste but make sure to clean all of the grit out or the cases may stick.
ETA- The Melonite treated chamber may get sticky when heated up the first time. You can clean the chamber with a good solvent or polish lightly but do not try to remove the black surface or refinish the chamber.
Oil the bolt tail and rings, drop of oil in the hole on the side of the bolt oils the ejector pin. Install in the carrier with the extractor on the right side looking from the rear. Work it back and forth in the carrier a few times. Oil the rails on the carrier.
With a mag in the rifle and no ammo in the mag, pull the charge handle to the rear. Does it lock back by hand?
If not check the follower in the mag to see if it will push the bolt catch up. There have been problems with the "BAD" ambi levers. If the bolt and carrier do not travel rearward enough the buffer or spring could be too long or the screw in the stock could be preventing the buffer from traveling back far enough. Is anything binding when you pull the carrier back and forth by hand? I found a carrier key installed with one side up on the rail of the carrier from the factory.
TESTING- place 1 factory round in the mag, chamber and fire it while holding the stock firm to your shoulder. Does the bolt lock back? If not it is short stroking.
When first testing newly built uppers and rifles always use factory ammo, Hornady 110-120gr. We use 120gr Hornady loads to set the gas port sizes with a standard carbine buffer and spring.
If the rifle shorts strokes when shooting factory ammo start checking things on the rifle. If it locks back on factory ammo but does not with the handloads then there is a problem with the handloads.
Be sure the rear set screw of the gas block is in the CENTER of the dimple in the barrel, that is why the dimple is there.
Short stroking could be caused by low powered ammo such as Remington when talking about the 6.8, in the 6.8 it is also common to see short stroking with light bullets 80-90 gr and fast powders using light published loads since many in reloading manuals produce 45-50000 psi.
With the 6.8 and the fast rifle powders it burns it is best not to use a H2, H3 or hyd. buffer or aftermarket springs. IF you want to use heavy buffers or springs you will need to drill out the port in the barrel to function with the heavier/stronger parts.
Keep everything lubed up well for the first 200 rounds but, DO NOT put a heavy coat of oil in the chamber or barrel, always run a dry patch through to remove excess oil.Port sizes for 6.8. If you are able remove the gas block and look at the soot ring(soot left on the barrel by the large hole of the gas block)
It should be completely around the gas port in the barrel. if it is not make witness marks with a sharpie to the rear of the port and align the gas block with it. While you have the gas block off check to see if the gas port in the barrel is clear, sometimes when they are drilled a small flap of metal is left hanging and when the first bullet passes it shoves it back into the port. On Mid length 6.8 systems using a car stock and buffer the port should be .076"-.078"(5/64) in diameter, rifle should be .093-.096. You can slide a 5/64" drill bit in a mid length to check and 3/32" in a rifle length to check. If you are building using an A2 rifle stock and buffer you will need to open the port up apx .004". Some new light bullet loads are even slower than before, those and Remington need a larger port to function. You can drill them out .004-.006" larger just be careful not to ding the barrel on the far side of the bore. IMO you should not drill ports or do anything else that is not reversible as a first attempt as finding a cure
. If you have an adjustable gas block drilling the port out a little larger isn't a big problem, just adjust it back down to obtain a 3-4 Oclock ejection.
If you are using handloads be sure your size die is squeezing the base down to .417-.420. Most chambers are .422 in dia at the base, some dies size to .422 and a semi-auto needs at least .002 clearance to chamber and needs .004" to be reliable when hot and dirty.
If the rifle in question is older the gas tube could be clogged, remove the gas block and tube assembly from the rifle and try spraying brake cleaner through the tube to remove powder residue. Be sure the gas tube is right side up.
Make sure the gap in the gas rings on the bolt do not line up.
.082"=#45 wire size bit
The chamber hardness will prevent anyone from removing any machining marks with a bore paste. Bore paste will remove the black and shine or make the surfaces sllicker but anything short of sandpaper run at 2000rpms for a few minutes will not remove any machining marks or grooves.
To test accuracy- Load 28.6gr AA2200 behind the Hornady 110gr HPBT to 2.26" then see below.