What I did in D123 is first make the cut, I positioned the pins inside the part, then subtracted the pins. The pins should align the two halves if the cut surfaces printed perfectly. I sanded the sides on a flat board to remove any high spots and the halves mate up tight. I just need to make sure it mates up good when I glue them. I will also need to measure it up good once I get the Z axis mocked up.
There is a Hacker Space in town I have always wanted to check out. I think they have a printer 🙂
Thanks for our input, that really helps!