First of all...Hey DynaMike fancy running into you here!!!
Okay, here goes...DON'T FORGET TO TEST SENSORS TOO!
Recently, my bike took a dump on me.
After running down the freeway, I turned off to surface streets and the engine just shutdown (lights still worked). I pulled over and let it cool and it re-started right away. It repeatedly shutdown and would not start (just "click-click). Then after cooling it down and restarting for another 4 to 5 times. Half a day later, I thought okay, it must be a coil problem. Repalced the coil still the same problem. I thought okay, it must be the module. So before changing the module I decided to put my stock setup back in. Still same shutdown. Then really looking at it again and found a shorted wire and bad battery. Fixed that. Then same shutdown problem.
Well...eventual FOUND the problem!
It all boiled down to a friggin sensor crapping out. The problem sensor was a Crank Position Sensor (CKP) of all things. The little piece of CKP is supposed to generate an AC signal to the module which references engine position (TDC) and engine speed...sounds like a part to make more money for HD. Hence, that is why it gave some symptoms of a bad coil or module...faked me out. This is the reason why I only used to like working on 'Old School' scooters. The little bugger CKP was intermittant and would only start to fail when the engine was good and hot...that is why it started when the engine was cooled down. The CKP actual counts 30 little teeth on the left side flywheel with two consecutive teeth missing to get a reference point established.
FRIGGIN SENSORS!!!
Also, if you ever think your carb is taking a crap on you...think twice!
Cuz there is also another little friggin sensor called a Manifold Absolute Pressure Sensor (MAP) that will affect timing (signal also sent to the module) and measures manifold vacuum. It could make you think your carb is wasted and ready for the swap meet basket.
But gee...if HD had it together, they could make it so you can hook the bike up to a diagnostic computer that would test all sensors. Guess that is the part where HD makes more money selling you things to fix a problem that really does not fix the initial problem.