I was working on a reverse situation (changing a 68 from standard to custom interior) in the early eighties. I can't recall whether the holes were pre-drilled in the inner door panel to fasten the standard arm rests, but I suspect they were. GM (Pontiac) didn't like spending extra money making two different kinds of things (like inner door panels) for options. I learned this when I changed a 68 Powerglide Firebird to a 3-speed. Under the driver's side carpet I found the hole in the floor pan for the clutch already punched and simply covered with a small tab of metal held in place by a sheet metal screw.
Another issue you're going to have to deal with is the different door opening assemblies, which attach and operate differently between the standard and custom interiors. In the worst case I suspect you may have to install clips (sorry, but I don't know what they're called--they're like a black phosphate folded-over piece of metal, open on one side with a screw hole centred on the other side. They slip over the edge of a panel and the screw hole aligns with a hole in the panel and provides something for the screw to thread into.
