So I have gotten all of the parts to the filtration system and I can now choose to oust Elder McNamara for Paladin Hardin. I have given Hardin all of the information to oust McNamara and he says to come back in a few days. I leave the bunker and wait for a week. Go back in and he tells me to come back later. I exit the bunker once again and fast travel to somewhere else and sleep there for a week. I come back and McNamara is still in control and Hardin is still telling me to come back later. Help? Am I doing something wrong?

I wish I could help,but I have exatly the same problem.Before ending the quest I′ve spend hours (real time),trying
figure out how to do the last optional part/talking.After fixing the filtration I try and reporting to Hardin,but he just told
me,-again,-to try and find some information.
After reporting to McNamara,and getting XP for finishing the quest,I talk to Hardin again,and also got XP for the optional
part.
It′s now more than 14 game days since I finished the quest,and I still get the message to come back in a few days,when I try
and talk to Hardin.

Aww crap,i just finished the first quest yesterday and i have been going back and forth every now and then and he still says to come back in a few days,i didn't think it was going to be a problem....damn,thats 3 missions today i have got that are bugged