I have overhauled hundreds if not thousands of cottered cranks. Certainly not a record, but enough so that I have established some methods and theories that suit me. They certainly differ from many other ideas and opinions but here they are for your reading pleasure.
First: When installing a cotter pin (or whatever you choose to call it) I PRESS it in rather than drive it in with a hammer or any other impact method. I don't know of anyone who still sells new presses. Park discontinued theirs recently. Used presses are getting a pretty good price on ebay etc. They are generally a heavy duty "C clamp" though I remember using some long, two handed, lever presses years ago as well. It can even be done with a bench vice though it's much easier to do with a hand held pressing device. Once the pin is pressed in, the washer and nut are put on and tightened firmly. Remember though, the pins are a rather soft metal, meant to deform slightly so as to mate nicely with both the crank arm and the spindle. Therefore, the nut can easily be tightened too much and twisted off. It is meant to keep the pin from backing out and not for pulling the pin in.
Second: Removing the pin can be challenging to many. There are differing opinions as to how this should be done. The method I prefer is to drive out the pin. I use a 12" long drift punch and a hammer. Start by lossening the nut about 1 full turn. Leave it on the pin though so there is a larger area for the drift punch to contact. The long punch helps me stay away from hitting the crank arm or the frame tubes when I swing the hammer. I never fail to dislodge a pin in more than two whacks of the hammer. It will usually come out with one good crisp whack. It is even more effective if the crank is resting horizontally on a wooden block such as a 4x4 about 12" long, sitting on the floor. Drill a hole in the top of the block for the cotter pin to fall into when it's driven out. Once the pin has "let go" the nut and washer can be removed completely and the pin will either fall out, can be removed by hand or gently tapped out. Cotter pins are not reused so there is no need to try and preserve the threads.
Some theories suggest that by hitting the pin with a hammer, the cups, bearings, and/or spindle can be dimpled from the blow. I doubt this simply because they are so much harder than the pin itself. Any damage to the bottom bracket that I've ever found has been the result of: 1)Normal wear, 2)Improper adjustment, 3)Lack of lubrication, 4)Rust and dirt contamination. If that is a concern though, supporting the crank arm on the wooden block means the impact will be absorbed by the wood rather than the bottom bracket. I am careful though, not to hit the frame, crankarm or my hand while swinging the hammer. The hand will heal in time, while the dent in the frame or crank arm will not.
Pins press IN very well but due to their softness, rust between the pin and crank, and the force with which they were installed to begin with, do not press OUT very well. They often will just deform and mash out causing it to "mushroom" making it more difficult to remove. Drilling them out is a lot of unnecessary work and if not done carefully, can result in damage to the crank arm from the drill drifting or being angled improperly. The crank arm is harder than the pin but not as hard as the drill bit. The spindle is at least as hard if not harder than the drill bit though so it is not at risk of being damaged by the drill bit.
Pins are available in a variety of lengths, diameters and tapers. The selection is getting fewer as time goes on, but most are still readily available. It is good practice to grind the taper of a pin if necessary so there is a sufficient number of threads extending beyond the crank arm for the nut and washer to attach while not having too much of the other end of the pin sticking out of the crank when it is pressed in. Pins are cheap so if it takes a couple of tries to get it right, it's not a big expense in time or money.
Servicing cottered cranks isn't exactly art, but it does require a good amount of understanding of the system and some sound training or experience with them to perform the task satisfactorily and without frustration.
Bruce Schrader San Francisco, CA
===== "Not all those that wander are lost." -J.R.R. Tolkien (1892-1973)