If the cotter pin needs filing, the first thing you will notice is it does not go all the way through the hole on the crank so that you can properly pick up the nut on the other side (don't forget the washer when checking this).

So that is where you start- to change the angle of the flat spot on the cotter, such that you get the appropriate amount of threads exposed once installed. Keep in mind that to install the cotter, a press should be employed. The nut is not to be used to apply the pressure of installation. Its there to keep the cotter in place once installed.

So its handy to use the press to see how much thread you actually have exposed when fitting it to the crank because you will likely have to install and remove the cotter pin a few times to achieve a proper fit.

Now the problem with this approach is that you don't get exactly 180 degrees out of the crank, but you can get really close such that you can't tell if you are simply careful. So how I would do it would be to file one cotter such that I get a good fit, then measure from the fat end (the end opposite the nut) to see how much you had to file the part, and then mark the second cotter such that you file it in exactly the same way. If you are careful and have a good machine scale it will work fine. A dial caliper is nice but not mandatory.

I just mount the cotter pin in a small vise and have at it. A medium bastard (flat) file should do the trick. Best to file too little rather than too much

Really, the thing you want is that cotter press. If you have one, you will really wonder how you got along without it. Bikesmith makes a pretty good tool at a reasonable price and I have used it on British three speeds, but also nicer cranks like Chater Lea, Stronglight and Campagnolo:

New Crank Cotter Press

Good Luck- have fun!!