Ok, In the rotor is a magnet. The picks up read this magnet to tell the coil when to fire.
As the magnet ages it gets weaker. If it gets weak enough the magnetic feild of the rotor can cover up the weak magnet, enough so the pick ups can't read it.
With your battery fully charged unplug the reg/rec connector, this disables the rotor. disabling the rotor eliminates it strong magnetic field so the pick ups can read the magnet. If this improves the way the engine runs you need to add a new magnet.
Radio Shack sells rear earth magnets. Item #64-1895 is a two pack of 4.5 mm/ 3/16 inch magnets for about $2.99.
Just "glue" a new magnet on top of the old one. Use any good heat resistant epoxy glue, I like JB Weld. No worry about clearance, plenty of room in there. These are very strong magnets and easily trigger the pick ups.
Leo