Okay, diving right in. The clone-centric corner of the fandom can be tricky to navigate for rare pairs, since most platforms surface the popular stuff. AO3 is your ultimate archive, but the tagging system is your real weapon. Don't just search for 'Clone Wars' and scroll. Try the 'Other Fandom Tags' filter and select 'Star Wars: The Clone Wars (2008) - All Media Types'. Then, in the relationship search, get specific but also broad. If you're looking for, say, Jedi Master Eeth Koth and a clone, you might not find a direct tag. Search for 'Eeth Koth' and then manually filter the results, or look for tags like 'Jedi & Clone Troopers' and 'Rare Pair'. Sort by date updated, not kudos, because those niche stories won't have the same traction. I once found a fantastic fic about Stass Allie and a medic from the 91st by searching the tag 'Clone Trooper Original Character(s)' and just digging through pages. It's a grind, but that's part of the fun. Sometimes you strike gold in a collection dedicated to 'Underappreciated Jedi'.
Fanfiction.net is harder, but not useless. The app is clunky, but you can search by character name. The issue is that rare pair fics often get buried under Anakin or Obi-Wan-centric stories. I've had better luck finding them recommended in the forums there, or in dedicated Tumblr blogs that curate 'rarepair' content. There's a blog called something like 'clonefandump' that reblogs a lot of obscure stuff. Honestly, Discord servers for specific clone battalions are the real hidden gems. People post their WIPs and headcanons in channels, and you can directly ask if anyone has written about, I don't know, Yaddle and the Wolfpack. It feels more like a community hunt than just using a search bar. You have to be willing to ask and engage.