In addition to my personal experience, I have encountered a photographer near me who has done the same thing that you are anticipating doing. He utilizes the same Condit punch that you describe.
The one other consideration that I might mention is that I found it important to incorporate not only pin registration of the negative in the carrier but also the negative carrier must be indexed into the negative stage of the enlarger. This becomes very important when one does multiple mask changes in the printing of an image.
In my enlarger modifications this amounted to "stops" on the two sides of the negative carrier with the negative stage of the enlarger acting as the rear "stop" for the negative carrier. I also incorporated a sliding/adjustable retainer that was incorporated in the left hand stop. This retainer utilizes three fine thread fasteners and firmly positions the negative carrier in the enlarger negative stage post in a repeatable manner.
Good luck. Masking allows one to take printing into new and exciting realms.