Would be alot cheaper if you designed a logo and incorporated into your pen blanks. They usually have small metal tags that can be added to a blank weather wood or acrylic. There have been a few people that have done that and become successful. They use better quality kits and go from there. Talk to Ed from Exotics if you are serious about designing a whole kit but be prepared to cough up some bucks$$$$$. Some incorporate the logo in the clip or you can have clips made for you. With soooooooooooooooooo many kits on the market why would you want to add another?? Not much has not been done already.
Easiest way to go - take kit parts, similar to what you would like to do, to a couple of local machine shops (shops that are willing to do small runs, many only take large or recurring orders.) Ask them for a quote and minimums for production.
Once you get a quote, ask them for the information they would need to do the work. You will probably need detailed drawings with measurements, at the least.
Come up with your design idea and then go to some of the CNC forums, there are some people with CNC set ups that will do small custom manufacturing jobs. Another place is the custom watchmakers, some have the CNC equipment that are capable of manufacturing small pen parts. Both places will have hobbyists that like penmakers are always n need of some way to make a few dollars to farther their own creative endeavors.