426 Timing question

So i have a 01 YZ426 with the baja designs light kit on it, so i put a WR flywheel on the bike. Now my understanding is that the TDC marks on the WR flywheel are not in the correct position in relation to YZ timing correct? When lined up where the flywheel said tdc i put a probe in the motor and the piston was not at its highest point... so i rotated it until it was and set my cam timing to that spot. Is this correct?

You did it in a correct manner, but I believe that you misread the flywheel. If you check it the way you did, then look at the flywheel and index mark in the case, I think you'll see that the mark farthest to the right on the flywheel is in fact aligned. The other two are a reference for ignition timing.

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