Hi Christownsme,
I've been a Type II BiPolar for half my life now; Delusions of Persecution were the first elements of the psychosis to emerge, and they emerged as a voice in my head that replied as "god" every time I prayed for help in dealing with the depression (and they were NOT nice!). My Faith was obliterated and my perception of God was so seriously warped by the time I received medical help that even to this day I can't read the Bible or enter a Church without becoming angry because for all my faith, my mountain never moved.
After almost a decade of this, I finally had to sit down and assess the reality of my situation: Being BiPolar was not a choice, I was created with it. God knows how my mood swings operate, why I have them, and how they impact my perception of reality and of him. The key thing I found was that through it all, I still believe. My core beliefs in Jesus remain intact (though not from lack of challenge), and thats enough for me to start again. It may take me the rest of my life to come to terms with my anger and sort through what is real and what is psychotic hallucination when it comes to God, but thats ok because regardless of the soil I'm in, I'll keep growing as best as I can.
The key, I think, for you, me, and everyone else here is that we all made a conscious choice to pursue God, and we did it when facing an illness that is considered one of the most psychologically and emotionally destructive mood disorders there is. It won't be pretty, and our faith may experience some ups and downs that would be considered horrific, but maybe thats why Jesus said that having faith the size of a mustard seed was all we needed.
When I get hit with the doubt and the anger in my depressive cycles, I try to mentally "step back" and remind myself that its my emotional state thats talking. When I start to pull out of the depression, I say a quick prayer of thanks that I made it through, and I think that God is infinitely happier than I ever could be that I made it through another cycle without hurting or killing myself. As for you: I'm willing to bet that God is just as happy when you pull out of a depressive cycle. Regarding your feelings of shame about the ups and downs in your faith: God knows whats causing them and he'll forgive them, assuming he even finds fault with them - he seems like a patient guy ;-)