I have a 6550K, ban model 20in with the 1/7 HBAR barrel (standard A2 style rifle). The barrel was threaded and an A2 flash hider installed but when the neutered FSB was removed the replacement's roll pin holes were drilled too high and it wouldn't fit the rifle.

Is this caused by a difference in FSB's between pencil barrels and HBAR's or did Colt do something silly with propietary FSB's on some of their rifles? I suspect, now that I think on it, that it was likely an FSB for a non-HBAR rifle however I'd like to know for sure.

Front sight bases are drilled for each rifle, if the replacement fsb was pre drilled 99.999% chance it's not going to line up with the old

So even though I went to a shop and tried to purchase as "new" FSB, since it was pre-drilled it either wasn't new or there are some out there that come that way? I assume that it's possible to order an FSB that has not yet been drilled then correct?

Yes you can get a non drilled front sight. http://www.bravocompanyusa.com/AR15-Front-Sight-F-Marked-p/front%20sight%20base%20-%20f.htm

Make sure you send it off to someone who knows what they are doing to get it installed correctly.

Thanks for the link Chuck.

It states that the "F" marked FSB is taller for use on Flat Top rifles, as this isn't a flat top I assume this wouldn't be the correct FSB for my needs right?

Your choices are slim for a non F front sight. It seems that is all most places are selling. The height difference is .040.
Try brownells or maybe bushmaster.