1- FHA is a big maybe- they'll want to "approve" the complex and many of the issues FannieMae dislikes may discourage FHA.
2- Portfolio lenders would fund this deal...with 20% down payment.
The only way around it would be a limited review questionnaire for the HOA which would have no reference to delinquent HOA fees but that would depend on the lender and what the loan approval says.
You have no obligation to stay with your current lender if they can no longer help you and as far as the appraisal fee that has to do with what was agreed on.
Other than Fannie guidelines there is FHA and portfolio lenders (savings & loans) that could be a solution for you but more information would be needed.
Hope this helped and good luck to you