the problem here is the quads, you heard they are good, but not realized why.
Well they’re good for texturing, but also good to follow shape, i guess you used some kind of autodesk product to get that model.
And not sure why but they tend to create terrible mesh layout, and small errors in hight, and small errors in corners result in strange effects. Often i also see poor connections in faces not realy connecting in such models (although they should) => verticles remove doubles as under edit mode often helps there.
a few options that might solve it.
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select all involved mesh areas on this flat surface, pres S for scale, Z for axis and press 0 enter, all must now be at exact same Z position.
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redraw the bad parts using blender, then you might put in a proper quad
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if its not for 3d printing, and it doesnt need to be watertight (cad models somehow often fail this to be often), then put a simple flat face over it, leave original mesh below.
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redraw the entire thing in blender, something i often did since the trouble as caused by autodesk programs often costed me to much time to solve, and it was often faster to redraw it (if you dont require an exact match of the given model).
