Hi -- Canadian in the US for a PhD here, and wondering about similar questions. NSERC income in Canada, and RA and small grants in the US.
I was told by the CRA to fill NR-73 to determine residency status (I wish I knew this early on in my grad studies), then fill the Canadian tax packages accordingly. In the letter I got back from them, I was referred to S5-F1-C1. Since I am a "factual resident of Canada", I then called the CRA, and I was told to attach the T2209 with my US income for each year of reporting, and attach a copy of my tax returns for each year. I'm still unsure about whether to include (sum up) my W-2 (income from RA) and 1042-S (fellowships) on T2209, what to put as amount of taxes already paid etc. And how to account for any taxes not withheld at the source (showing up on W-2 and 1042-S) but that I paid to the state or IRS after filling my US taxes....
Calling the CRA today and hopefully I can update with some answers.
PS: If that is helpful to anyone reading, if you are still contributing to your TFSA in Canada but wrote a departure date in your tax returns my mistake or misunderstanding, you will be taxed a lot on it so get that checked!