I know it is a bit obvious but S&S ProTune2 is a very useful tool for diagnostics. Even if, like me, you are not that good with the technology and a bit reluctant to try it, it is worth connecting a laptop to the ECU, checking the fault codes and testing the outputs if you have a problem.
A friends M3W engine suddenly went to very rough running and was difficult to start requiring some throttle to get it to start at all, usually you never touch the throttle on starting. On running ProTune2 there were several historic fault codes but no current ones. We cleared them and tried to run it again to see what came up, nothing shown after a few spluttering seconds of running.
You can access less with a locked ECU than you can with an unlocked one, no bad thing normally as that makes it almost impossible to do something wrong. This one was locked. You can still access the “Test Outputs” from the Options Menu. For those that have not used this feature it allows you to check the ignition on both cylinders one at a time, it sparks a plug held against the cylinder for 5 seconds. Fuel injectors can be run independently for 5 seconds, you can hear them or remove them and spray the petrol into a jar to check the spray pattern. The fuel pump can be run for 5 seconds and you can check the pressure with a gauge at the test point at the same time. The Idle Air Control can be motored open and closed. You can also test the Tacho, ECU and Check Engine Lamp. It doesn't test everything, Throttle Position Sensor, Manifold Absolute Pressure, Air Temp and Crank Position are not there but it does check the fuel and sparks are there.
All the tests passed apart from the Idle Air Control Valve that “failed test” consistently, it also sounded rough when motoring. A new Harley Davidson IAC p/n 27628-01A was ordered. Once fitted it all fired up and ran perfectly. I know it's not always that easy but at least you can test a few things easily with ProTune 2.