I'm pretty sure that NGUI keeps everything scaled so you can directly use mouseDelta without any scaling under normal circumstances. However, if you're dealing with a situation where the ratio of the camera's orthographicsize isn't 1:1 with the camera's pixelheight in terms of world units per pixel square, you'll find that mouseDelta is then 1 unit <> 1 pixel. Again, normally this shouldn't crop up, but you said you did some customization, so you may have introduced a situation where the ratio of units to pixels isn't 1:1.
For what I'm working on I needed to be able to drag around a map area where grabbing a specific visible object and dragging it would result in the result of the object's coordinates *exactly* lining up with the cursor as it is dragged. For this you have to calculate the ratio of world units to pixels.
On app startup, and whenever the screen size changes, I call something that includes this:
pixelsPerGridSquare = 1.0f / (_mainCam.pixelHeight / (2f * _mainCam.orthographicSize)); // do this as an inverse, so just one division
Then, in my mouse drag handler I have this:
mouseDelta *= pixelsPerGridSquare;
The result is that the mouse drag in pixel (screen) space is properly scaled into the scene's world space and the calculated position deltas for the gameobject (or camera) transform lines up visually with what you see on the screen in terms of mouse motion.
