I swore I created a thread on BF once showing how I file cotters. It's killing me I can't find it.

Bikesmith used to sell cotters and may still. Closest I can find to explaining filing. Like, go here: http://www.bikesmithdesign.com/CotterPress/cotters.html

Look at the picture of the three 9.5mm cotters. The one on the right is what most of my machined cotters looks like. I'll give my first press. If it doesn't go in fully, when I pop it back out, I can see how far down the face it's hanging up. Then I'll start filing so it's moving closer to the face of the middle cotter, then press in again, if it doesn't seat far enough, I'll pop it out and check where it's hanging up. Rinse/repeat. by the time you get to the facing you see on the far-left 9.5mm cotter in that pic, I'll be surprised if you're not seating fully where you need to be