I read somewhere that you might not have a good connection beneath the ECU and the heat sink. You may need to scuff up the 2 pieces with some 3M green pad or light sand paper and place some special heat sink dielectric compound between them to help ensure a good ground as well as heat conductivity. You can find the stuff at any computer parts store.
Man I hope that works. The thread stated everything that happened in the order it happened and all events were one right after another, not days apart, and read as:
1. Riding home, bike started fine and ran well then complete loss of spark.
2. Engine would turn over and lights worked.
3. Engine stopped responding altogether.
4. CAN LINE error message appeared.
5. Called Dealer, Dealer recommended a tow home.
6. Tow specialist came out and could not get bike to start, CAN LINE error still displayed.
7. At home read a bunch of threads.
8. After deciding upon a course of action. Pulled ECU and noticed some oxidation between the ECU and heat sink. Lightly sanded base of ECU til shiny and sanded heat sink plate.
9. Tightened down the bolts that held them together.
10. Turned key on, no CAN LINE error displayed.
11. Hit starter button and the bike came to life.
He should have put some sort of grease in there to stop the oxidation from recurring. Not saying that your ECU or heat sink are all corroded but did you make sure they were absolutely spotless before joining them? Supposedly you lose the ground that powers the ECU if not making good contact. I've not done a full swap myself, again why I do feel Service Shops can have a benefit even if expensive, so I'm not sure what was involved in the ECU swap. But bad grounding seems to be a recurring problem with CAN LINE issues, along with melted wiring harnesses from other issues. Being that you did not mention letting the smoke out of the wires, keep that smoke in there it's what the electrons jump across to get the electricity to flow, I'd be leaning more towards a bad ground at the ECU. Even the screws/bolts holding it down might need a little attention. Basically just make sure any contacts you changed are in good order. Also check all around the engine to make sure you did not knock any wires loose, especially around the ground wire coming from the battery. Also make sure the battery connections are good and tight.
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