Mike,
Congratulations on your marriage and child.
Obviously, it's (long past) time to stop neglecting your documentaion. You've created some needless complications for yourself, but with patience and effort, they're not insoluble.
First, get a CPF. You could have done this the day after you arrived in Brazil, and don't need a CRNM, the new ID card for resident foreigners, to get it. Just go to the office of the Receita Federal in Recife that issues them - you should be able to walk out with it. Unless your Portuguese is flawless, I strongly recommend bringing your wife along, and for her to do most of the talking. There may be some concern about your expired visa, but stressing that you're married here and have a Brazilian child should get you past that.
Next (really, pretty much simultaneously), start your permanency process with the Federal Police. Get ALL the documents required for your situation on the Federal Police website - the image you want to project with a yearlong overstay is that you're the most compliant foreigner EVER. Getting your Canadian docs legalized by a Brazilian Consulate in Canada will be complicated, but other Canadians here have done it. (Unfortunately, Canada hasn't joined the Apostille Convention.) Canadian docs will then need to be translated here by a Sworn Translator for presentation. Again, your wife should probably be your spokesperson. Once your application has been accepted, the Federal Police will give you a document that serves as a temporary ID until your CRNM is issued. With that and your CPF, you can open a bank account, buy property, and pretty much do anything a Brazilian citizen can, except vote.
I'm a great believer in the power of smiling and begging with Brazilian officialdom, and by all means, give it a try - but the R$10.000 is probably gone, gone, gone.
While you're getting paperwork, get a SUS card for the national health service, too. You can get them at most state clinics and hospitals, it's free and same day.
As the husband of a Brazilian citizen, you may, if you wish, become naturalized one year after the issue date of your CRNM, and become a dual citizen. I understand, though that the Tax Treaty between Brazil and Canada is a very advantageous one, so most Canadians opt to remain permanent resident foreigners. You'll want to see how you'll be affected before making that decision.
Good luck. Please keep us posted on your progress.