Getting the flywheel out where you can work would be a big help. What is this fly wheel off of?
Most manual flywheels for the old Chevy sixs that I have worked on have the hole drilled and tapped all the way through.
If so you may can drill from the back side with the drill press. Might get lucky and the bit catch the bolt and take it right out.
If you have to drill the hole bigger, then heli coil it so that you can go back with the same size bolt as the rest of them.