To answer your question, YES, Motion Windows in Vancouver WA can custom fabricate a window to your specifications, they did for us.
Here's their Site address: http://www.motionwindows.com/
We had our cockpit windows replaced due to creeping seals. The original windows had the dividing bar between the top pane and the slider directly in our line of vision. On the new windows had it moved up about 6 inches, works great and we have a taller slider.
The shop is family owned and operated by Tom Kemp and his sons. They do professional work. The cost for both of our windows including installation was $1,200.