Maybe I don't understand the term of "custom cue" .. but if it is a custom to your specs, wouldn't any maker provide a pin that you ask for, since they are making it custom for you?
Having said that, most high end custom makers, especially at the level of money you said you were willing to spend, have a LD option or very high quality, straight grain shaft that they offer with their cue. If you have a shaft that you plan on mating to the butt you are willing to buy, I would suggest sending it to the custom maker to match it up. If not, I would see what comes with their cue and seeing if it is something you would like.
As far as my very humble opinion is concerned, as far as feel, it's like 30% tip, 30% shaft, 15% joint pin size, 15% joint setup (which includes not only base material but also ivory sleeve over wood, brass inserts, etc), and only 10% butt. Once again, only in my opinion, the butt alone (not talking joint pin, joint material, or joint connection) is mostly about what you want the cue to look like.