If AC has EDIFACT through check, they can add your onward flight info into you checkin for both bag and boarding pass purposes. This will send a message to VA who would confirm you as a PAX and AC could then also issue the boarding pass. It is not so unusual to have onward connections on different tickets. I believe they will let you go if that all works . . good luck with this and all the posts above have covered all the main points. At least you must give the flight info and your VA ticket number to AC so they can attempt to get the boarding pass and bag tag correctly printed.