My first house purchase had original windows from the 60's; single pane, rotten sills, etc. I am not sure how custom your windows need to be, but we had a window "guy" come in and measure every window in the house for replacements. I dont believe all were off the shelf sizes, so some had to be somewhat custom. I believe I payed somewhere around 6 grand for 24 windows and replaced them all myself.
In the long run, a better option might be to go new construction and adjust the framing to fit a standard size. This will require trim and siding work alongside whatever framing adjustments are needed. For example, you might find a standard size window is 1" wider and 1" shorter window with some easy adjustments and come out ahead cost wise over custom windows.
My wife and I have used buildzoom in the past to find a general contractor that can handle jobs like this.
EDIT: I also posted earlier in this thread about my excitement of hitting my first pick and pull after a number of years. I was able to get all the large items on my nitpick list for less than the cost of a used ebay dome light (dome light, radio bezel, OE bottle jack, random hardware, couple pigtails, relays, etc). Very happy!