AKA: Out, damned NOTP!
The first step on our journey to getting to sorting out the tags you don’t want starts here on this FAQ archive from AO3 itself. First and foremost, you need to get the userscript add-on/extension that’s appropriate for your browser. All I see is for Firefox or Chrome, so that’s what you get.
Now! I’ve got Chrome, so I grabbed the Tampermonkey extension. After you get that open to this screen (click on the black box with two circles to the right of your address bar):
You’ll go to the AO3 Saved Filters link on the AO3 page. Open the code tab, copy the entire code, and paste it into your extension. Save it, and refresh/restart your browser.
Head on over to your particular fandom on AO3! We’ll go by Attack on Titan because I’m a fucking nerd. So, just opening the SNK page gets us to here as of this posting (8/19/14):
What’ll we search for, then? Let’s say…a yumikuri story, that’s it! So let’s enter the main filter of “Krista Lenz | Historia Reiss/Ymir” in the sidebar to the right.
Notice that “Saved filters” thing above there. Let’s open that puppy up.
I haven’t totally tested the Global tags portion because, let’s face it, we all care way more about the fandom part of it. So! Per the instructions on the filter script page, let’s filter out every story that also tags “Levi/Eren Yeager” in the pairing tags.
Remember to save before you move on! After you save, click the Sort and Filter button to see your results.
Ding, results! Let’s keep filtering out just as a final test—let’s get rid of “Marco Bott/Jean Kirstein” to remove that top story to check.
And save ‘n’ filter~
I…well, I don’t know what that top story is doing there, but you can see that the desired yumikuri pairing is still in the second story.
And there you have it! Play with the tags as you want to (especially because none of us agreeing on a spelling for certain names or ordering for the names), but this seems to be working! It might be overzealous, given that it took some ten thousand stories when you removed the first pairing, but hey, better than a fuckin’ poke in the eye.
Have fun filtering!