First up, if the ECU needs replacing it gets replaced regardless of mods. Send me the last 6 of your VIN and I can check for you. Haven't seen any Rockets recalled in Aus with this issue (yet) - only Bonnes and 1 T'bird.
Secondly, your problem, even though it's mostly better, seems to be most likely spark related. Check leads (high and low tension) for good contact and plugs. Also check there are no splits or tears in the insulation on the high tension leads, especially around the rubber ends that go over the plugs. These can tear when pulled out (well, one of mine did).