I am going to go out on a limb and ask if the flywheel was installed correctly? If there is no spark and the sensor voltage is that high then what I mention may be irrelevant; however, if spark is present then it is possible that it is being delivered at the wrong time. If the flywheel was not indexed to clyinder 1 TDC then your CKP signal could be off by 60 degree increments for 6 bolt mount or by 45 degree increments for 8 bolt mount. You did mention that it ran before you performed the gear box repairs, my thought circles back to flywheel and it's position so, is it possible to have inadvertantly misaligned it upon installation?

The CKP sensor is not that difficult to exchange however I would think that the voltage output is indicating that it is working well enough to operate. Have you tried a coil?
Just another .02