Head unit should look as stock as possible? that's rought. She could do a JL Cleansweep, and use the auxiliary input for her Ipod, it will maintain the factory CD player and clean up the output, adjusting equalization to +/-3db from 30hz/20khz, however she still won't be able to play Mp3 cds.
as far as speakers go, there are literally dozens of great brands, and hundreds of less than great ones. You can do a nice 6.5" component up front, a 5x7 coaxial in the rear, on a good small 4 channel amp.
as far as subs, you could do a single 8" sub ported in a very narrow enclosure, just depending on your preference.