Will I be able to stay or return to Zion after I finish the main plot of the DLC or should I get all the unique stuff before I finish?

You can return to Zion.

From what I gather you can still return to Zion but whatever quests you did not do the first time 'round will be lost to you. I'm not however, sure of this as I am still trying to pay for this DLC through Steam. Not having broadband and using my Android tethered to my PC svcks.

i tried to get unique service rifle after finishing the main quest and it wasnt there, reloaded save and went back and it was there. think u gotta get it b4 u finish main quest

I believe a companion with you can pick it up. If that's the case and you finished the main quest you've lost it unfortunately.