i'm not sure of the definition of 'scrupulosity' and i cannot diagnose you with anything... i have manic depression and it has caused me to grow stronger in my faith in many circumstances. i also probably have at least slight OCD... this can cause intrusive thoughts and i'm wondering if this is along the lines of what you are experiencing.
we all struggle in our walks, it can be difficult to have faith when we feel cut off for whatever reason.
i'm not sure i have the answer for you, but you could see a psychologist to rule out or otherwise confirm whether you may struggle with OCD or manic depression. personally, my bought with manic depression has further confirmed my faith, yet i deal with symptoms of OCD where i have intrusive thoughts that i don't even really consider my own.
it's difficult to know what is going on, i think, unless you seek the care of a qualified psychiatrist in the area of discerning whether or not you struggle with mental illness. aside from that, i think we all have ups and downs and can waver and have weaker and stronger seasons of faith.
that is all i can think of to say, if something else occurs to me i will try and respond.
if any of this sounds redundant or obvious, i apologize. i just think it best to probably see a doctor if you are really struggling with inner turmoil that you are not certain about, just to be more clear yourself about what is going on.
there are people who will tell you ' it is all spiritual, you don't need doctors or medication. ' now i am not suggesting you need these things, i am only commenting that some people do need the support of specialized care and must be on medication to be able to function in a more stable manner. i cannot determine whether this is the case for you, as i have said... but it may be worth seeing a specialist just to narrow down what it is you may be going through and perhaps rule out any mental illness.
that said, yes... i do believe everything has a spiritual basis to it, but- if we are sick and need medication... such as someone who is diabetic needs insulin shots, or an amputee could need a prosthetic or a wheelchair, then we need to address these physical issues.
from there, knowing whether or not you need medical care or what kind... you can supplement and add to what you are experiencing by seeking support from other believers and doing the regular thing of reading the bible and prayer, perhaps attending a church and also clearing your life out and discarding things or behaviors that could be getting in the way of your relationship with our Lord.
Sounds like The Spirit is working just fine inside of you. But I agree that if you are in fact officially diagnosed as having bipolar like me then chances are you'll need some medicine to help with that. Like Lav said, see a psychiatrist and get diagnosed.