At this point, connecting NYP to GCT would be most feasible and easiest if the connection was made to the tail tracks that the LIRR is using. Unfortunately, the tracks from the LIRR level will not connect to the Metro North tracks, meaning that the train would end up in Sunnyside and not headed towards Montreal.
I'm not sure that with the new lower LIRR level that it is even possible anymore to connect to the MN levels from the South. Between the Lexington Avenue Subway that transitions between Lex and Park Avenue at GCT, the #7 Line below that, the Times Square Shuttle above that, the loop tracks for MN, and the Park Avenue tunnel for cars, I don't think that there is any room to shoehorn in another tunnel anymore.
So the only answer might be that after connecting to the LIRR tail tracks, make the stop on the LIRR level, and then find someplace north of GCT to build a connecting track between the LIRR tunnels under Park Ave and the MN tunnels above the LIRR tunnels. I'm not sure if that is possible, without taking out a building basement however. It may be, I just don't know.