TournamentsPro can Automatically Pair Competitors for Individual Tournaments.  Boat Numbers and Flights can be Assigned for Individual and Partner Tournaments.

You control the number of boats per flight and TournamentsPro will rotate the flight assignments from tournament to tournament.  It can also check the tournament history to prevent repeat pairings.
Boat usage and pairing with non-boaters is also rotated.
(View Sample Pairing Listing)

Once pairing has been performed, changes can be made to the Boat Numbers or match-ups for any last minute roster changes.