I can feel your pain, I had exactly the same issue when I bought my JDM . There is no way of changing the current equipment you have to work. I have just had the screen taken out and had a touch screen installed in the cubby. It looks totally stock and works great . I have taken the DVD unit out from behind the drivers seat (just need to find a blanking plate now).
If you look up Custom Sat Navs in the for sale section you will see what I have had installed (mine was the first one to be done, by Nurrish). If you are anywhere near the Midlands fitting is included in the price as well.
Quick question for you, is your cubby automatic? Mine goes up when the ignition is switched on and drops again when turned off. Not many around if you have that!!