Welcome to the forum.
Without seeing exactly what your dealing with, about all I can do is to give some thoughts which may not have much to do with your problem.
Think of sand cast parts as the 'rough stock' that something is going to be made from.
That said, not only will a number of surfaces need to be sanded and polished but they may need to be filed to fit together properly.
If the lugs are rounded or tapered and that is causing the concern about starting a drill bit to drill thru them then the surface should be filed flat so the drill won't 'walk' away from the location it needs to be.
This shouldn't be a problem if the filed flat will be hidden after the cap box is installed into the stock. No one will ever know about it except you.
Before drilling the thru hole for the lid's pin make sure it is fitting the way it should.
Any material that keeps it from fitting properly should be filed off.
A good vise may be needed to hold the parts before drilling them and it will probably be difficult to get them held without using some wood shims between the jaws of the vise and the cap box so get creative. Make some wood shims so that the parts are held securely in place.
If you can post some pictures of your parts and the problem you are having maybe my answers will be more directly aimed at the problem.