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Mike,
By "return loop pulse" you mean the pulse from the disc and your optical fork, I believe? Yes, it has to be full amplitude, should always drive the full zero to 12 volts. The schmidt trigger is a good fix for this, but it's also possible to do it with careful positioning of the fork and a good disk.
Have you been trying to work with small sync holes? They do not have to be small at all, because the 4046 is edge-triggered - it won't care if the disc pulses are wider than the sync pulses. The scanning holes need to be small in order to get good resolution, but the sync holes can be big to make sure you get plenty of signal out of the fork. Also, you could elongate the sync holes radially- they could look more like slots so that the fork position is less critical.
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