You set Facebook app to sync with your Existing Contacts only, that's on Facebook app under settings - App settings. Just go to your phone Accounts under settings and check that the Sync With your device option is checked, while you are there click on the account so it syncs again.
On your Contacts app you click More, and there you see Merge contacts, that will merge al the contacts it finds that matches between all your accounts, then click Settings, and you'll see Contacts to display, when you click that you'll see that by default it has All contacts selected, so that's the reason you'll see all your Facebook friends on your Contact app, I hate that and I don't want it or need it, so I just select my Google Account and it will show only my contacts under my Google account, you can use the Customized list of you want to see more than one account's contacts.
Then only thing left is to go to your Contacts and see which one are merged automatically the rest you should do it kauai, you need to go one by one and edit them and click on Link option and it will allow you to manually choose the other account's contacts to link to.
I hope you can finally do what you want because the above is as much detailed as possible.
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