I'm pretty sure that the CMP sensor is only used at starting and disregarded once the engine is running. Once it knows cylinder #1 is on TDC compression stroke, it can keep track with just the CKP sensor after that.
This is borne out by the Fail Safe chart in the service manual.
I first became aware of this when working on my Aprilia SXV. It is a V-twin with only a CKP sensor. The ECM throws spark at both cylinders for about 20 seconds and then figures out which cylinder to fire by the pulse intervals. A not uncommon mistake on those engines would be to install the cams 180 degrees off. It would start just fine and run for 20 seconds
I just don't see how a faulty CKP could produce these codes on those two cylinders so consistently. Even the manual's possible "things to check" does not mention the CKP as a possible culprit.
"Ignition coil, wiring/coupler connection, power supply from the battery"
I know it has been checked, but my guess would be the that there is a poor connection on the O/W power wires to those two cylinders. At a certain rpm, it might just vibrate the poor connection enough to trigger the fault.