Need help: How to drill holes in aluminum pax car shell for hand rails, ladder rests, etc.?

Put a strip of masking tape where you want to drill. Mark your hole locations and use a centerpunch to dimple the aluminum so the drill bit wont walk. 
For small holes, just drill em by hand with a pin vise and the appropriate drill bit. May want to start a drill or 2 smaller than what you need, its easier to make a hole bigger than smaller.

My method would probably be to start with a pin vice and tiny bit to make sure my starter hole was in the correct place.  Once you have the hole located, you can step up to power drills.

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I would use the methods mentioned as far as measuring. But seeing you only have one shot at this. I would get some thin aluminum. Say 1/16 thick and lay everything out on that as far as holes. Drill out your markings.  When your satisfied to how how it looks and everything fits. Use that as your template on the car itself.

@OGR posted:

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Thanks. 

And thanks to all who offered suggestions.  I'll incorporate all of them when I try them on a donor aluminum shell that I have on hand; plenty of room for practice.

Now if i could just find some nice brass or 3D printed vents.