I have a copy of Melodyne that will take MP3/WAV and do most of what you want - I have not loaded it yet but my source reckons it is excellent and he is a guitarist. PM me. I might just load it and try. He raves about it. It apparently produces notation.

In my experience with these things, you do your thing, then realise artistry is about bending the rules just enough to flummox any precise pattern recognition system. So you have to tinker before entrusting to notation and Melodyne allows you to do that relatively quickly, he reckons.