Another way of registering your negatives is to mount the original in a larger piece of film of the same thickness. This will then allow you to use a larger punch and registration pins for the project. You will no doubt want to mount some form of a step wedge into the process to allow you to control exposure and processing of the separations. By mounting your original into a larger piece of film you can also add a small step wedge along side of the original. If you use just the 35mm original you could have the step wedge showing through the sprocket holes of the transparency.
Gord