Start with the basics, Do a leakdown or compression test, check all initial settings like plug gaps, distribitor cap and rotor arm are correct, then check ignition timing and fuelling are all correct.
The flywheel wont have any effect on power output, the camshaft certainly will, so also try to ensure its the right one for your application.
What you will notice with a lighter flywheel is that acceleration in gear will be faster where a heavy flywheel will result in a slower in gear acceleration, thats due to it resisting being accelerated, refer to newtons laws of motion..
You wont have the same torque in higher gears as thats precisely what occurs when you make the gear longer, less torque but higher speed, lower gear gives higher torque but lower speed.
Make sure all the basic stuff is correct with the engine firts as its the source of all your power.