| If the bolt isn't structural, the there's no problem drilling them. I had a 500 Pantah, originally prep'd by Paul Klackeiwicz of DTS, and every thing that could be was drilled, cross drilled etc. even down to tapering the heads on cap head bolts.
Easiest way is to set up a collet in a lathe and drill through so to keep it dead square. | 
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