Have you been pre-approved yet?
Get ready to write letters, I found it easy to have a template letter. They would come at me with some transaction four or five months ago and say why did you transfer money to another account or I was given a reimbursement check from my work, they would come back at me ask if it was income. I'd have my canned letter ready type in a paragraph fire it off to them asap.
I would say the best defense you have in being self employed is time. Under writter wanted to see I was employed under the same job title for 3 years, so i'm sure the same would apply for you.
The mortgage guys are hungry nowadays, rates have risen not as many refi's to go around.