Personally, I would not. You're opening a can a worms you won't be able to $hut ea$ily w/out lot$ of $$$ ($ubtle enough
).
Bose does some funky things when it comes to the resistance in their speakers (among other things). Improvement in sound will be negligible w/out also swapping out the dash, door and amp to Bose so everything matches up. Not 100% certain as to cost, but I think from the factory Bose is something like a $2K option. Aftermarket, I'm sure it'll be at least that!
To get bang for your buck, especially since you already replaced the h/u, is to upgrade the remaining speakers in the car to good quality components. Go w/ either coaxials or components in the dash and upgrade the doors to 6.5", 6.75" or 6x9" (w/ their metric equivalent
). You might even have some $ left over from your original $900 you were going to spend on just the Bose parcel shelf if you DIY.
Here's an excellent guide on how to from Andy_M over on Renntech.
Andy-M's Guide to Ugrading Boxster Sound System
I'd suggest getting speakers that match up well to the amp you have or a new one you plan to get.