and I wanted to know if anyone had any tips for clearing out the emotional side of indoctrination

How does on clear away emotions? It's not easy.

I still have hang-ups over sex based on my Christian upbringing, and I've been an atheist for roughly 15 years now. It's not that I don't rationally understand the roots of my beliefs or why I'm wrong about them, but the emotions don't just go away because you wish at them hard enough.

However, it helps to have a support system. You need friends who will urge you to do the things that you should do, and who will restrain you from doing the things that you shouldn't. I don't believe in the efficacy of Alcoholics Anonymous, but one thing they did right was to pair you with a "buddy" who you can call on when you need help. It just shouldn't be another person who is also struggling with these problems :p