It's pretty amazing I posted a request for help and got more messages than I've ever gotten from a story. I've deleted that blog post, so i don't keep getting answers.
The question was, when submitting .txt file how do you preserve italics. The answer is:
_italics_
*Bold*
_*bold italics*_
And this information was in the authors section the whole time, i just couldn't find it at midnight last night, too tired i guess.
With that solved, part 2 of John the genius will soon be posted.