AR Front sight
Ok, is the front sight assembly canted to one side or the front POST bent? Front post is an easy fix. Front sight assembly cant is a larger problem.
One full revolution of the front sight POST equals 5 MOA of elevation change. One A2 front post click equals 1 1/4 MOA up or down. (old A1s were five clicks, one MOA per click. They kept the screw pitch and tossed out a detent notch) One click on the rear sight windage is usually 1/2 MOA movement.
If the post is bent, replace. Rock River has them for 2.50. The smaller diameter match posts are more, but not more than 15.00. Bent, polished, or mushroomed posts shouldn't be tolerated. You can rotate the bend toward you or away, so it won't be leaning left or right, but that's a field-expediant temporary fix. Straightening the post with pliers will break it.
With a proper post, I'd set the rear windage to Mechanical Zero. (middle of the hash marks on the back of the rear sight base lined up with the line on the top of the flipped-down peepsite. Some folks rub white-out or white paint into the lines and wipe off the excess so you can see them better.) Set the elevation at 3/6, (if marked) or two to four clicks up. Shoot a careful group off a sandbag and bench at 100 and see where it is. Repeat a couple of times to make sure your benchrest technique is good. I'd use a standard NRA 100 yard rifle bull and a 6:00 hold.
If the group is off 3:00 or 9:00, see if the windage knob will handle it. If it won't then the front sight assembly may be a problem.
Handle the elevation with the front sight post. Some folks like center-mass holds, some shoot 6:00 holds. (You can't set it for one and shoot the other without adjusting your rear elevation.) If the group goes in the middle, then this is your No-Wind Zero. The No-Wind zero is rarely the same as Mechanical Zero. (My service rifle No-Wind 200 yard zero is: Up 8, Right 2, for 69 Sierras on 26 grains of Varget. This sight has half MOA elevation and 1/4 MOA windage. )
If you can't get a No-Wind zero with the rear sight windage knob at 100 yards, then there is a problem with the front sight base.
First check to see if its broke/bent/cracked. If it's really gotten canted there is probably physical damage. It is a pretty easy replacement. The pins drive out TO the left, I think. Google up a schematic. You can always use a brass hammer or screwdriver through the sight base to try and move it, but if its moved very far, it's probably broken/bent.
Old time rifle range Sgts used to put the end of the barrel through a hole in something and bend it to fix radical windage problems. Don't do that.
The pins are going to put it where the pins are. Period. I'd forget filing. If replacing I'd get the allen-screw NMC front sight base. You can take all the cant out and (nearly) put your No-Wind zero at the Mechanical Zero.
I'd pass on screwing/unscrewing the barrel. You have to go all the way to the next gap for the gas tube. Replacing the front sight base will require unpinning the gas tube first from the front sight base. It's easy after you have done it once.
I'm sure this is too long, but I'll wrap up by saying that the M16A2 sight system is really pretty good- nearly match-grade. Properly indexed it works very well. (The only rap is the short sight radius, but at Camp Perry, the AMU was shooting 1000 yards with them.) It's the best standard iron sight system by any contemporary military.