Just wanted to let you know how we resolved this situation.

We were never particularly thrilled about the Montreal scenarios, and after a lot of searching, we were able to find a return trans-atlantic flight from Madrid to JFK on Air Europa. It requires a 2nd switch in Europe - basically, our stop in Montreal is being replaced by a new stop in Madrid - but the connections have more buffer time, which makes us feel more comfortable. Also, in the event of a delay or problem, we're going to be connecting relatively early in the day in Paris and Madrid - airports with many direct flights to JFK (including flights on Delta).

At this point, my only concern is schedules changes, especially since we have so many connections. Also, I don't know that much about Air Europa, but hopefully they don't decide to stop flying to JFK or something like that.

Final Itinerary is:
JFK-BOS (Delta)
BOS-CDG (Air France)
CDG-LJU (Air France)

LJU-CDG (Air France)
CDG-MAD (Air France)
MAD-JFK (Air Europa)