As you suggested, that Form 1099-R seems to have the wrong amount in boxes 1 and 2a, so you should contact the payer about this. It would probably make sense to request a filing extension at this point, but you still need to pay your taxes by April 15, which you would do under the assumption that you will receive a Form 1099-R showing the entire $3,439 in boxes 1 and 2a.
