Hi,i take it you are using the 6V batteries and equipment,so it may be worth checking you are getting the full 6V during starting,and then a reduced voltage,via the ballast resistor,at ignition "run" position.
If the ballast resistor is damaged,bypassed,or not in the run circuit,the coil may be receiving full voltage,and after a prolonged period,could cause overheating of the windings,and other issues.
I have had similar problems on old machinery,and trikes,etc,where the clue is a burn on touching the coil casing.
Some ballast resistors are part of the loom,and the direct full voltage is derived from either a feed from the starter motor,or the ignition switch direct,but if the coil is rated for it's 100% duty cycle at reduced voltage,it won't like full voltage.