Couple things to note:
- The Reaction Rod is great for a lot of things, but it should be understood that using one in this manner is simply transfering the same torque used on the flash hider to the barrel extension. Barrels should be clamped, not held by the extension.
- The order of operations in making a barrel relies on a proper and permanent torquing of the barrel extension. The gas hole and front site alignment are indexed off the TDC of the extension, which requires the extension remain absolutely fixed in place once torqued. In almost all cases of extension removal, especially after an improperly torqued extension has come loose, the gas hole and front sight will no longer align properly.
Think about it. If the gas hole were drilled with the extension torqued at, say, 90 pounds then the extension were removed and retorqued to 150 pounds, the gas hole will now be pointing somewhere to the upper left rather than straight up. A few pounds of difference is all it takes to cause misalignment.
That barrel should not be repaired but replaced.