Simple Man...
The best you can do with how much glass ends up above your window opening when the glass is all the way down will depend on how far down the glass (and what holds the glass) can go until it contacts the bottom inside of your door. If there is anything you see that can be trimmed or adjusted to get a better result, give it a try but don't expect too much.
I see the measurement you took and just remember you will also have an inner door panel with upholstery that will be up little higher than the inside door panel, so that measurement will become less when you are finished your build. All side windows on these cars will be exposed some when down so don't be too concerned. You appear to be in the ballpark.
You are doing a great job.
RT