So if I understand you correctly you have, as you said, striped some of your car to bare metal and some not. Then you did some body work on I assume the bare metal areas and then sprayed the Blitz Black directly over this with out priming the surface. Correct?
I am assuming that you feathered out the edges of the body work and remaining paint properly.
If so, what your seeing isn't so much different levels of the surface, but rather different areas that the paint has soaked in more than others. This will leave a drier look over the body work and old paint areas, and more shine over the bare metal areas creating different textures. This gives the viewer the illusion of different surface levels. It even feels different when running your hand over it, which also gives your hand the illusion of different levels. It takes a bit of time to train your eye and your hands to see and feel how straight a panel is rather than see and feel the texture that can fool you.
The way to prevent this would have been to put two nice even coats of filler primer on the entire car and resand without breaking through to the sub surface.
However, now that you have sealed it with the black you can go back over the car with a red etch pad (don't break through) and reapply two more even coats of paint. This should help even out the look of the surface.