Haha, I thought so. You either use the Bose system or replace it altogether.
That setup should sound pretty good.
Since there are 9" woofers already in place, that leads me to push woofers larger than 6.5" to increase up-front midbass.
As for the dash openings and replacing the Bose system:
If you don't want to use a 3-way front, then you can probably fit many large format tweeters up there that play lower frequencies than typical small format car tweeters to raise the soundstage.
Large format tweeters:
http://www.zaphaudio.com/tweetermishmash
Seas tweeter TBFC/G $32 each
http://www.madisound.com/cgi-bin/index.cgi?cart_id=7818521.9143&pid=1005
with
Dayton Reference 8" woofer RS225-4 for $43 each
http://www.partsexpress.com/pe/pshowdetl.cfm?&Partnumber=295-376
$150 for a killer front 2-way speaker setup that will sound better than many overpriced car audio component sets.
Or you can go with the higher priced Morel Supremo SW 9" woofer and Supremo or Supremo Piccolo tweeter.
http://www.morelhifi.com/products/mob_components_woofers_supremo.html and
http://www.morelhifi.com/products/mob_components_tweeters_supremo.html
You'd want to drive them actively with a 4ch amp and a HU with built-in DSP crossovers like an Alpine CDA-9835, Eclipse CD8455, or Pioneer P880PRS. You can hook up an iPod to any of them via Aux input. They all have the upper line DACs, 6ch DSP for crossovers, EQ, time alignment, etc.
The Bose rear door speakers ran off the HU power for rear fill.
The rear d-pillars left alone.
Hmm, let's see if I can build a lower budget rockin' active system with sub:
Pioneer DEH-P880PRS $325 shipped
http://www.onlinecarstereo.com/CarAudio/ProductDetail.aspx?ProductID=16945
Seas tweeter TBFC/G in the dash $32 each
http://www.madisound.com/cgi-bin/index.cgi?cart_id=7818521.9143&pid=1005
Dayton Reference 8" woofer RS225-4 for $43 each
http://www.partsexpress.com/pe/pshowdetl.cfm?&Partnumber=295-376
Elemental Designs 12" sub 13Kv.2 dual 2 ohm for 4 ohm load at $125
http://www.edesignaudio.com/edv2/product_info.php?cPath=21&products_id=31
or one of the hard to find Image Dynamics IDQ12v2d2 subs on eBay
http://cgi.ebay.com/Image-Dynamics-...ryZ18803QQssPageNameZWDVWQQrdZ1QQcmdZViewItem
Alpine MRV-F345 at $279 shipped for tweeters 75w and sub 300w
http://www.onlinecarstereo.com/CarAudio/ProductDetail.aspx?ProductID=14928
Elemental Designs Nine.2x at $265 for midbass 200w x 2ch at 4 ohms
http://www.onlinecarstereo.com/CarAudio/ProductDetail.aspx?ProductID=14928
I'm pretty sure both of those amps will fit in the open space.
Sound Dampening ~$150
http://www.raamaudio.com
Wire, Cables, connectors, etc. from:
http://www.knukonceptz.com
and
http://www.partsexpress.com
One kickin' SQ system within $1500