I hear you. I've got a deprogramming project of my own. I've got this girl I know who's trying to argue Thomas Aquinas's five proofs as being some sort of sound argument. I can feel her questioning her faith. When she feels the need to start looking for apologetics to bolster her faith, she's breaking out. I just need to work with her a bit more on the logical fallacies and see if I can demonstrate why almost every argument out there falls into an Argument from Ignorance, at some point. Of course the others fall apart in some other way, but it's amazing how many include that simple, basic fallacy.
When you can point to somewhere in every argument and say, "And this is where they start making shit up," surely she's got to open up and admit it, eventually. If she was still at the point where she thought blind faith was a good thing, it would be hopeless, but she's looking for logical evidence.
I feel both your pain. I too have a "pet case", but it has long since proven in tractable.
@ Michael: I think it is inevitable that (eventually) lesser ways of thinking will fall to the wayside and the best ones will stand the test of time. I loved this sentence of yours in particular, "So much improper programming has been done and the neuronal tracts solidifying the convictions have been potentiated for years and years". So much damage...
@ Joseph: Want to switch pet cases? Lol, jk. Yours at least sounds marginally hopeful. Mine asserts that faith is at the root of all beliefs. His argument isn't poorly-thought out. Since our experiences are fallible, and we never know anything absolutely or without any doubt at all, then it takes "a leap of faith" to begin trusting our senses and our experiences and everything else which builds upon them. Despite the deepest epistemological arguments that I can muster, he cannot be swayed from this belief. Thus, faith is categorically justified, and this supports all his other beliefs. Maddening!
No, mine's cuter.
Ugh, yeah, I hate that sort of nonsense. That's borderline solipsism. It's not about absolute certainty; it's about a preponderance of evidence. When everything that's turned up by science flat-out contradicts the things you have faith in, it's a good bet that your faith is completely misplaced.
Admittedly, this leaves you open to the God of the Gaps stuff, but essentially, after something fails like that 3 or 4 times in a row and needs to go find another gap to hide in, you chuck the whole thing and go find something else to believe in. Eventually, you'll hopefully end up at skepticism, after going through 3 or 4 faith focuses.