Depending on the Non-O you start with you may need to apply for your 12 month Extension of Stay with 2 or 3 weeks left on your original 90 day entry stamp. Check with the Immigration Office you will be aplying at (when you get your re-entry permit maybe) what their requirements are well before you exit the country to be aware what will be required on your return.
You've already been told no. Get the money deposited ASAP so that 2 months after (seasoning) you can apply for your 12 month Extension of Stay (not a Visa)