Hi Mat, an O-scope would probably be the most efficient means of checking the ECU - especially if there happens to be an ever so slight malfunction of any component. It could be an irregularity with a number of components - leads (you could use an ohmmeter to check for resistance), suppressors (same procedure), spark plugs (clean or replace), distributor cap and rotor button.
The 'O' scope will give you cylinder comparisons as well as the function of electrical components, but I suspect you may need a competent mechanic that can actually evaluate the readings provided by the 'O' scope. Keep us posted if you can regarding any future findings. Regards Styria