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feed aftermarket EQ (quarter din Kenwood in console), amp and speakers from line-level out of the stock head unit (if there is such a thing).
No there isn't such a thing. They make the reverse with an aftermarket head unit feeding the existing bose speakers and amps. This can be done on C5 but not C4.
I'll also add a CD changer through an FM modulator.
This will work but it will only sound as good as an FM radio station and not have the CD quality. You will loose highs and lows, especially with the limited FM of the stock radio.
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92TrippleBlack is right on both counts.
You have the right idea about bypassing the Blose amps and dropping aftermarket speakers in the Blose pods but you need to go one step further and get an aftermarket HU as well. You won't be able to run aftermarket speakers off the Delco/Blose HU. The only thing that won't look "stock" is the HU. You can still use the stock speaker grills with most aftermarket speakers.
Aftermarket amps are optional. ;)