The only thing I would hate doing this is that on the EX's there is a steering wheel radio control (up, down, station switch) which would be sitting there useless

Check out our FAQ on the subject here. If you can isolate the Honda button leads, you can use a variation on the stalk interface to go directly to the Empeg's serial port. I'll look at the link you supplied in the follow-up message and see if it's worth adding to the FAQ, too.

figure out some way to input the empeg into the factory system via some sort of aftermarket cd changer interface.

Or just buy an aftermarket CD player with a line-in and put the two in the dash together like dionysus did in his Honda. Or have only the empeg like I do in my Honda.

You're going to get the best sound if you use an amp and your own speakers in the Honda. I will warn you that running the cables to the trunk is tricky, but the cleanliness of the resulting job is worth it.

___________
Tony Fabris