If you have either of the Special Settings or God Mode switched on, any difficulty you had played since then won't count, and you'll need to replay them. Starting stock can be changed.
Of course, make sure to start from Level 1.
It's been a while since I attended this guide, I need to work on explaining some of the others, but it has gotten to the point where I can no longer push forward due to my average play. I'll work on it soon...