I think that you should figure on between $50k and $55k out the door. I had our boat rigged at the factory with the Wallace heater, shore power, a Norcold fridge, extra lights, a cabinet with drawers under the helm seat, extra 12V and 120V outlets and also had them install the sonar, GPS and VHF radio I purchased. I also had them install Scott downriggers, a camper back and twin Honda 40's. By the time I got fenders, lines, downrigger balls, rod holders, etc. I was into it for about $55k. In principle, many of the things I had the factory do I could have done myself and saved considerable cash - in particular the wiring. In practice though, a number of planned add-ons and mods haven't gotten done due to limited time etc. However, at this point, and knowing what I know now, I wish I had done the wiring myself - I think I would have done a cleaner job, I would have labeled the runs in much more detail and it would be easier for me to maintain and modify now (I also would not now put the battery switch on the bottom of the starboard lazarette).
However, when I bought the boat, I was completely clueless about boats. It is only through reading on this site, experience with the boat and carefull thinking that comes after having the boat awhile that I now know how I'd rig it if I had to do it all over again. One thing I'd do for sure if I was you would be to attend a C-Brat gathering prior to ordering your boat. Interview people to find out what they'd do differently and take careful notes of the mods that you see that you like. That will allow you to get the boat outfitted closer to what's ideal for your needs at the very beginning. Just reading on this site can help alot too. I wish this site was available when I started looking at C-dory's, I would have made some different choices in the initial purchase.
Roger on the SeaDNA