Components needed to upgrade your shields and weapons are gained in new game plus. Defeating as many Last Ones now actually helps you. You're good, dude.
I beat the final boss in the first playthrough doing all of the main quests, side quests (minus two that are in the Dead Dunes), and most of the Canvas of Prayers stuff ('bout 60 out of the 80 or so available). On Day 9, you'll get something that links the cities together and makes Soul Seeds easier to farm for, if you care about that. You have plenty of time of just standing around or sleeping in the inns, or maybe looking for any treasure you may have missed or any outfits, adornments, weapons, or garbs you haven't bought yet. Just a lot of checking around for anything you missed when you just want the end to come already. You are all set, buddy.
There may be an additional ending or so that only comes with a new game plus, but don't worry about that (I honestly don't know at the moment), but that can't be helped. You're ready to save the world and all'a dat.
Not too long ago, Origin downloaded updates for my Steam copies of Mass Effect 2 and Dragon Age: Origins (I was able to redeem their Steam codes into Origin since they were EA games, not sure if that can still happen these days) and rendered them unplayable (read: couldn't start). Had to verify my files through Steam to get them working again. Thankfully, whatever mods I had installed for Dragon Age: Origins didn't have to get re-installed again.
Just make sure to turn off automatic game updates to avoid stuff like that. Of course, that'll mean you'll have to keep up with games that regularly get updated these days like Battlefield or SimCity, but you're probably safer with older games like the ones I mentioned.
Drew and Vinny have the most games that also appear on my list (three each), but only Patrick had Fire Emblem: Awakening on his which is the truest Game of the Year. I guess Jeff's is also similar to mine since I don't have The Last of Us on mine by choice, but we only have two games in common (BioShock Infinite and Gunpoint).