When dealing with cross-border taxation issues, there are three easy steps.
- Lie down on the floor and cry
- Realize that no one cares more about getting your taxes right then you do, the internet is full of crucial info but also misinformation, and even so-called experts may be wrong about complex situations
- ????
I'm still on 3 for my own cross-border woes (aka how the **** do I invest as a Canadian resident but dual citizen) but I'll throw some ideas your way.
The US and Canada have a tax treaty that means that Canadian earned/wage income can be excluded with a direct deduction up to ~80k USD. I would guess something similar applies the other way. So declare all income on both, but you should probably have equivalent deductions on all foreign income. You may not have to file Canadian taxes if you resided in Canada less than the US and earned no income but may need to for credit reasons. (honestly who knows but I'd play it safe and file in both places)
You file basically at the same time for both... you might be able to claim tax paid/payable but it doesn't depend on filing some first (and as above dual income taxation is avoided through the tax treaty). I'm guessing you may only be able to claim the deduction from a country on that's country return against income in that country. That seems sensible.
As for MFS vs. MFJ.... not sure but I would go with whatever you did previously in the states for you and the IRS's sanity, unless a tax professional tells you otherwise.
Speaking of which....
get a tax professional who specializes in cross border tax issues unless you have no other option. It will cost money and suck but if you do it for 2016 you avoid issues that could haunt you later. Also, if you or your wife are US citizens, you are in for a whole world of hurt (PFIC, FBAR, filing taxes with the IRS forever etc). I hope not for your sake but speak up if otherwise!
Good luck and please update us as it goes :)