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The lower blind holes should be filled and new lower holes drilled.

Measure twice inside and out to make sure the holes you drill will not interfere with the bottom of the splashwell including the washers in the link you showed. Green holes for sure but maybe the Yellow?

3 holes up is all the way up. Bolt in bottom hole for your motor.

All the way down is NO holes up which is what you have.

Edit:
See the holes on this members personal page he drilled for his new E-Tec.
https://www.whalercentral.com/infusio...ser_id=291