I was looking for something similar. I found a $400 steel frame (on sale, swobo fillmore) that fits with fenders, disk brakes and shimano 8 speed. Then I put on a dynohub, lights saddle and pedals from old commuter, new PDW rack and Soma handlebar. final tab was $1K and I went through a local bike shop so that includes labor. The only upgrade left will be tires, but I'm going to wear out the kendas it came with first. The 35s I have on the old commuter wont fit inside the new fenders, my only disappointment in the build. I like big comfy tires.

The fillmore comes in a mixte frame, the company is no longer in business. You might be able to get one for less than the price on the website by asking.

As mentioned, you can always go one upgrade at a time if you start with the right bones.