Upgrades are usually per direction, not including stopovers. Once she stops in PBI, that ends the upgrade. It would be a North America upgrade for PBI-YYZ.

I believe CO said they'll be participating in the *A upgrade program, but that's only full fare, and it may not be immediately.

I would look at CO's discount BF tickets. They're sometimes not much more (or even cheaper) than Full Fare Y.