I wanted to add more to my thoughts, now that I am not typing on my I Phone.

It is true that I had to have 2+ bikes that were wrong before I knew what was right. Because of what I learned here, I was able to do a lot of after the fact changing of components on my current carbon bike to make it fit well. My first 2 road bikes were bought when my DH was in a more "hard core" almost racer phase and we both have learned from my experience. My custom bike was built and purchased with a specific purpose in mind. I made some decisions that the shop owner didn't like, but the builder did it all. I still want to change my bars, but after an initial getting used to period, I am riding each of my bikes about an equal amount of time.
I am not one to freak over the prices you quoted. My non custom carbon bike cost 5K, 6 years ago, and my custom ti bike cost, well, more than that. Close to the range you were quoted but not quite as high. But, I never would have spent that amount of money after only riding for 1-2 years. My first road bike cost $1500 and the second cost about 3K. I've been riding for 12 years, I do a lot of hill riding, I'm short (5' 1"), and I would never spend the money for electronic shifters. Unless you have an issue with your hands that makes it physically difficult to push the lever, it's a crazy added expense. "Clunky" shifting sometimes is a result of user inexperience, although it can be crappy components. But really, shifting is an art and eventually, it becomes intuitive.
Personally, I would go for the stock bike, in your position, and really think about the extra added expense of the electronic shifters and the expensive wheels. My personal opinion is that unless you are racing, you don't need either right now. Ride for a couple more years and think about what you really need in a custom bike before you buy it.