Convert to a transverse mounted I4 engine with transaxle gearbox for best reduction in drivetrain power loss...
Flywheel is a great mod, I've yet to do it for the FR-S, but do plan on it...won't ruin daily driveability. Had an 8lb ACT Prolite in an Integra before and it was perfectly well mannered and daily driveable...even in stop and go traffic jams. Lot more getup and go in the first 2 gears....2nd gear was a blast!
Other than that the only other things possible for driveline loss reduction is the driveshafts, bearings, and fluids (engine oil, transmission, and differential)....