I missed your original post, but I have some experience on this topic that may or may not be relevant to your particular situation, but here it is anyway... Drilling the flywheel to "factory specs" (diameter/depth/orientation) often leads to vibration. I am unsure if this is because of operator or equipment, etc, but it rarely seems to work well. Here are two good ways to balance a neutral flywheel properly to factory spec:
1: Buy a counterbalanced flexplate (there are a couple companies that make them) and sandwich it between the flywheel and the crank. It sounds horrid, but there are very reliable accounts of this working, although I haven't tried it myself. There was some discussion about bolt lengths and starter shimming, but even without shimming the whole thing was reported work well.
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2: Buy/borrow same said flexplate, sandwich it to the flywheel 180* out of phase, and have the machine shop balance the whole assembly to neutral. Once you pop the flexplate off, your flywheel will be balanced exactly to the "factory" spec. I have done this several times, and it works great, and is very easy for the shops to do. Same theory applies to any cast crank external balance engine.