You totally did the right thing, upgrading your sound system aftermarket will blow the Bose sytem away. The system is way overpriced IMO and doing some research online will point you in the right direction on your choices.
Take a look at lots of the installs on this forum, read their feedback. Look at the online stores they shop at and saved tons of $.
Good luck, I personally am looking into the Eclipse 726E a new head unit for 09 that has been highly rated by consumer reports/ Cnet reviews/.
Priced at $1000 on
Woofersetc.com the online car audio super store, the largest selection at the lowest prices!
I had JL Audio XR components in my old 350 and they were excellent. May try something different this time around. Maybe Boston Pro Se's