I have an upper with a barrel that originally had a standard fixed FSB. I removed the FSB (drove out the taper pins) and have been using a low-profile gas block (screw on type) on it for a while now. I'm pulling the FF hand guard to use on a new upper build so my question is how likely will it be that I can re-install the original FSB (with new taper pins) and have it come out properly aligned?

As long as you didn't enlarge the holes in the FSB during the removal process, or damage the taper pin grooves in the barrel, you should be good to go.  I have done it for several customers that wanted to change out the handguards for a free float system.  If the holes in the FSB have been damaged I just tap them with a 8/32 tap and use headless set screws to reset the FSB.  Once you have done it a couple of times it's no big deal.

Same sight, same barrel? You don't even need new taper pins. They are designed to be removed and reinstalled.

Thanks gents, I appreciate the replies.