Your jumped through all the hoops and got an engineering degree. Now you are scared to drill holes in a door? This really makes me think about this situation.

This is a simply new thing for you to learn. As above do the 2 end holes first. Having the holes too low is the only problem. Having them off sideways makes no difference. Having the end holes slightly too high doesn't matter, file them lower to have the trim fit at the correct height. Then do the center ones after the end 2.