I have an assembly that requires around 4000 holes mostly going through 2 to 3 sheets of 10 ga. sheets (every sheet is entirely different) and I am wondering what is my best option to make all these holes (so they all line up as well)?  I have been using hole wizard thus far....but as my drawing has been loading for the past 8 minutes I am guessing this isn't the best option. Maybe I need to turn the rebuild upon opening of file off... I don't know, but my current scheme isn't working. Any suggestions?

Update: I tried uploading the assembly but its too large! Go figure...