I was going to try the drilling before I did the paint work, but the amount of adjustment that is available on the first gens is crazy. Imagine it as working in 4D.
We ended up taking the hinges off and putting them back on a number of times and figured out that it does not take but a very small amount of movement to throw everything off. So I didn't feel like drilling a few small alignment holes was going to be very beneficial for my situation.
In the end I felt better about understanding what adjustments were necessary to move door to the right place. I found that by using a regular pencil and marking around the hinges that I could get everything in position.
This is why I chose to shoot thru out the area and then reshoot again after the doors are on, and then clear.