http://partsfinder.onlinemicrofiche....ION%20FLYWHEEL
Looking at the parts fiche I assume you mean the 3 bolts that hold the starter gear to the flywheel. From what I can see they have no other function than doing just that.
The flywheel is pressed/pulled onto the crank in position with a keyway. If you didn't remove it I doubt that is your problem.
One thing you have done is remove a lot of rotational mass. Is it possible that you are feeling that? What exactly is a poor bottom end?