You can't turn a non-refundable payment into a refundable payment with greater usefulness than the original form no matter what you do. If you purchase a refundable ticket for $400, using a $350 voucher, you will receive back a $50 refund to your original form of payment and a reissued voucher for $350, with the same expiration date.
I would call AA and ask for an extension based on the time it took to get the voucher to you.
Administrative fees will depend on the specific fare conditions but are generally US$0 unless stated,