Now that you have the correct scale size and pattern of what you want to build make yourself a cutout pattern that you can use in cutting your materials. Cut the actual doors & windows out of the pattern in a piece of card stock. Cut these pieces to the exact sizes & shapes that you want for your finished project.
These patterns for cutting the materials will be used when it comes time to cut the materials for your actual structure.
I like to use different color card stock for different parts of the process, that way there is no confusion as to what is used for what. In this case I used blue for the initial mock-up for sizing, scale & structure look. I used yellow for the pattern to be used for the cutting of the materials. Also with two different card stock if I mess up the one for cutting by cutting into it or damaging it to the point it no longer is effective I can make another using the original pattern to keep my project moving forward without a lot of wasted time.