I'm converting from nothing in particular at the moment so I did have these 'dark thoughts' as you called them until recently. And I realised this, scripture must be read as a totality, the second you do that is the second that they begin to make sense. And to quote St. Agustine, 'I would not believe the gospels were it not for the authority of the Catholic Church'. That is to say that the fact that the original apostles, those who led the early Church and claimed to have witnessed the accession of Our Lord into Heaven, were willing to die for what they saw, rather than sending others to die todos them, proves the validity of the resurrection of Jesus to my mind.
If you want to start practicing again I can give you a link to a set of Catechisis tapes made a 20 or so years ago by a priest who converted and, through these tapes, inspired me to convert.