The rules also give notes about integrating a regular LANCER game with the fleet rules - have players control their parent fleet in the Battlegroup system, but when a boarding action affects the ship their pilot party is on, have a corridor-to-corridor fight using the regular LANCER rules instead of rolling for the success of the boarding action!Okay.
I have a number of earlier space battle rule systems. I suppose I can always use another! The setting is intriguing as well. I am definitely enjoying your battle report / story hour!
Alternately, if the LANCER player characters are represented by an Ace Squadron (as is suggested), instead of rolling for the Ace Squadron's boarding attempt on the enemy flagship, have a LANCER fight instead! Fun times.