I just got my Bushmaster 16" upper back from a warranty replacement of the barrel.  The flash suppressor is noticeably off (not TDC).    Rather that send it back again, I ordered a wrench, barrel vice jaws, and new lockwasher from Brownell's.   Is the removal/installation of flash suppressor fairly easy.   Does the gas tube have to be removed to use the barrel vice jaws?  

When you say not TDC, do you mean that you do not like where the slots are positioned.  A factory crush washer will usually have a little indexing left.  In other words, you usually can get at least another 45 degrees.

Do not know anything about the barrel vice.  I change a FS by having a fat soft-assed friend sit on the rifle while I take a strap wrench to the FS.  I do not know of an easier way.  If you care about your rifle, be careful about the friend you choose.

If the FS is on a pre or a no ban gun it should come off with a simple end or adjustable crescent wrench. You should not need  barrel vise jaws for this. If I read your post correctly the top of the FS is not at the 12 o'clock position. All you need to correct this is a 'peel washer' set to control FS timing.

If looking down the muzzle at the flash suppressor, the suppressor is canted slightly clockwise.  I have a Colt and another Bushmaster of which both suppressors are perfectly aligned.   My guess is that it will not affect shooting enough to notice but the military armorers' manual and other reference books I have read say the middle slot should be TDC.  

I put all my FH’s on hand tight with the armorers wrench. If you don’t have an armorers wrench use a 19mm or US equivalent open end  wrench to brake the FH loose holding the rifle in between your knees. I’m guessing you have an A2 FH and from your description it’s over clocked. Loosening the FH then re-tightening it to TDC hand tight may work. Let us know.