TM47 is for 90 day reporting, what you need is TM7, which is for yearly extension of stay... you should include all the school papers and your copies of workpermit.
To add more, once you submitted the form, ask the officer if you need to re-submit them every time you do your 90 day report.. there are "some" immigration office that "requires" you to submit the form every time you do 90 day report or extension. and also, you need to write down all foreigners living/staying on that house/property.
I am thinking also that he got a wrong visa (non immigrant visa) then when he tried to extend it, the immigration told him he got the wrong type and can't extend unless he has paperworks to extend it as explained by the officer. He was given an option to do a border run (get a visa exempt by crossing the border) or just pay the 11 day overstay on the day of his departure in December.. still, a photo of the visa itself would be nice.
but it only works on Internet Explorer and from time to time it goes offline. :) and if your info is not yet on their database, you can not use the system.
that's the actual fees and doing everything by yourself with correct papers... doing it with a lawyer or any agency, might have different price...(service fees) for their "work" in processing your permit... (possibly)