Trying to figure this out myself as well. It seems like the best solution is to leave the original head unit in, remove or relocate (as in behind out of sight) the CD player (don't yet know if it can be totally removed), and add in a second stereo that is single den. I would get one that has the nice 7" screen.
I believe that new wiring has to be run to all the speakers because the original unit uses fiber optics. NOTE: The fiber optic wires do not need to be kept in a closed loop as many believe for the car to start, it is a copper connector in the original head unit that acts like a fuse (but not a fuse). Running new wire would be a good excuse to get some new speakers too. I'm assuming original amps would still be used.
IDK how to get the car dings and alerts to work though, I believe they run through the original. Maybe they plug into the original head unit and can be switched over?
I would still rather replace the original head unit, even if it meant forging a custom face plate from black fiberglass. Because I think the original looks like sh*te..it looks like a computer from 1983. But apparently the process of doing it is ridiculously painstaking.
Let me know what you find out.