Here's the low-down: lowering the weight of the drivetrain components will show as an increase of power on an inertial dyno. So like you said, lighter flywheel will show an hp increase. Other things that I know of which would show such results would be pullies and a knife-edged crank.
I doubt the motor mounts would help for any power increase, as they certainly have no role to play with the drivetrain.
front end alignment. excessive toe (either + or -) would have an effect, how much i don't know. low front tire air pressure should also have an effect. higher air pressures reduce rolling resistance. last time i dynoed i ran 44psi in the front tires