Been thinking about this for a while. many of whats been said is good advice. A couple of things spring to mind.
Partially blocked tank breather? This may cause restricted fuel flow after the 60 or so miles as a vacumn built up? Any air noise when filler cap removed? If fuel flow restricted same as excess air - either situation would show up via the "fuel trims" readings. this could be determined from live data feed via the EOBD socket into a scanner. I think unlikely as a lean code would come up i think.
Its stated the engine runs fine even thought the light is on. My best guess in this situation is you may have a lambda probe / 02 sensor ( in the exhaust) thats dodgy. Again this canbe checked via a scanner that monitors the sensor voltages - it should vary as the engine is revved - a steady voltage from an 02 sensor indicates its dead. This would ping the EML light on and the engine will still run ok as the ecu compensates.
Agree about battery voltage - modern cars are very fussy with to regard volts - even if the cars starts ok it might still have a dodgy cell causing havoc. best bet is try another battery if its more than 3-4 years old.
I know a new coil has been tried but I'd still not rule out a connection to or the coil itself. maybe breaking down as it gets hot? Was it a good, known make or ideally genuine Ford? Are the connections to it clean ( inside the connector plug) and tight?
I would pop a set of iridium plugs in to be sure as well. ( wolf performance sell these for the Sigma engine).
Before you go replacing more bits i think best bet is to get a decent scanner ( not a basic code reader) onto the car and have an in depth look at all the live data readings - this should help point you in the right direction.
One thing is for sure - its fixable!
2015 Morgan 4/4 (Wolf tuned)
R56 Mini Cooper S and
Quite a few BL relics too.....