Thank you for the advice. I just bought a spring loaded tool similar to the Pin Vise to place an indentation to where I will be drilling (General Auto Center Punch). This was found at Ace Hardware.
I'm using an electric Dremel with the required sized drill bits to drill 2-56 holes in my styrene shims and the floor of the boxcar. The floor feels like tin metal or delrin plastic.
I want a 2nd 57' mech reefer car but the thought of going through the conversion ordeal again wears me out.