I have completed the battle with the spirits in the Priory, and talked to all of the knights, including the Shield quester. I have all of the relics except for the shield, but when I click on the "map" while activating this quest line, it only points back to the Priory of the Nine, rather than to the Fort Bulwark site, and Fort Bulwark is not on the map at all.

I know, after reading the wiki, the general location of the Fort, but I'm worried that I somehow glitched this quest. Shouldn't the Fort be marked on the map?

You should get a green/red arrow if you have the Ft Bulwark portion of the quest (Wisdom of the Ages) selected as your active quest. The actual fort will not appear on your map until you are in range of it. This quest does not automatically pop the fort onto your map as many quests do.

The quest did advance once I found the fort, but I never got an arrow until then. Just as in Fallout 3(Although exiting/re-entering the game usually fixed this in FO), I think this kind of thing happens map-wise, but doesn't really affect the quest itself, unless I'm wrong, which I'll follow up to announce, maybe. hehe.