This post is mostly to write down everything in one place for me to review it.
Tracer 900 (2015), lost compression, went to dealership for assessing, came back.
Swapped engine. Old loom and coils used.
Reconnected everything and refilled fluids etc. Recharged battery.
On starting up, ECU reports error codes 33 and 34. Yamaha & Haynes manuals both show this is “Ignition coil: open or short circuit detected in the primary lead of the ignition coil for cylinders 1 and 2”. No other errors including coil for number 3 (would be error code 35).
Coils have a primary and secondary lead. One lead is the same colour on all three (red/black) and proven continuity from coils 1-2, 2-3 and 1-3. Other lead is a different colour for each. Proven continuity from each of these back to the ECU connector. Continuity fails from red/black wire on all three coils back to the ECU connector, this includes coil 3.
Swapped coil 1 and 3, same errors on ECU.
Followed manual’s instructions to clear any errors, errors do not clear. Unsure if this means it is unable to clear error or it won’t clear errors that still exist.
Do not want to refer to dealership as they seem to have fucked me in another issue.