I'm not sure where that information is stored, but what you wish to accomplish can be achieved from within the IS console while playing the game.
I'll explain how to fix the location of the Port UI, since that one is straight forward:
First, run your port script so the UI loads.
Next, in the console type: UIElement -list
That will list all the UIElements weather they are visible or hidden. It should show something like;
Top-Level UI Elements
----------------------------
frame 'main hud' - Shown
window 'window selector' - Hidden
window 'radarconfig' - Hidden
window 'radar window' - Shown
window 'port' - Shown
window 'console' - Shown
tooltip 'auto tooltip' - Hidden
Your actual UIElements may vary, but as you can see the UIElement 'port' is what your looking for.
Now that we know the name of the UIElement, we can move it around. Try something like:
Code:
UIElement[port]:SetX[100]
UIElement[port]:SetY[100]
Which will move the port window to the top left corner of your screen.
Mad Hatter wont be as easy to move around, as its actually loading a bunch of different windows, even tho only a few are visible when it starts. But the method for doing it is the same as your port window. Start with UIElement -list and you'll see all the windows it's loaded. Assuming they are all off screen, you will need to individually move them the same way you did with the port window.