I cured myself and married Aela. I don't get well rested anymore, just rested. I don't get lover's comfort either. Is it permanent side-effect because I was a werewolf before? Or is it because I married Aela?
What does it say under Active Effects? There's a bug where you'll wake "rested" according to the screen, but it will say "Well Rested" under Active Effects. If you aren't getting Lover's Comfort, talk to Aela. Say you'd like to move to her place. She'll say she'll meet you there (her place in Jorrvaskr's basemant). Go there and the quest updates "visit your spouse's home." Now talk to her again and ask to move wherever you want. Spend the night with her there and you should now get some lovin'.

Also, to the main topic, I rather wish there had been some closure dialog with Aela after the brothers are cured. Something like, "well, Aela, you are the last werewolf of the Circle. There'll never be another like you again." Then she can agree that the tradition of the Companions takes precedence, and that she's glad you respect her personal choice.