I had the same exact idea and interest as you do right now 1 year ago. I have all the info you need. And lucky for you i save all notes and pics from my projects.
What you want to do will cost you about $200, and is well worth it. You can do the install yourself.
The best 8" replacement subs for the Shaker 500 subs would be the Shelby subs. There compatible in size/ohms and sound incredible. You can use the same OEM shaker 500 amp with the Shelby subs (and the 2 sound awesome together!). There $139.99 right here.. 05-09 Shelby/Kicker 8 Woofer Kit for Shaker 500/1000, Pair 05-09 Shelby/Kicker 8 Woofer Kit for Shaker 500/1000, Pair [KA-8-WOOFER] - $139.99 : Shelby Performance Parts Discounted by Champion Mustang, Shelby Parts, Shelby GT500 Parts, Shelby Super Sn
Then for the 6x8 door speakers, the best compatible ones are the Kicker KS680 6x8 speakers, and i did the homework there, SonicElectronic is the lowest price for them at $86.96 found here KS680 | Sonic Electronix Search
The wiring adaptor to make life easier (get it!) is the Metra speaker harness 72-5600 for $12.99 found here Metra 72-5600 (met-725600) Speaker Adapter for Select Ford
And if you really want to add some nice clean base, i found a custom 12" subwoofer made for the Conv 05 Mustangs. It fits right in the trunk back corner and takes up no trunk room. But gives you a 12" in that trunk. And you can still fit stuff in the trunk, a must have item as i see it! Ill supply all the info on that if your interested, like where to buy, wire colors for the rear speakers to tap into for the sub..etc.
Ill add some pictures in the next reply, i need to make them smaller to attach to a reply. But i have pics of the speakers and finished product installed.
MAC Stainless axle backs & Prochamber
JLT CAI w/ SCT tuner
CDC Classic Chin Spoiler, TruFiber GTS4 Hood
Aeroform Sport Bar (in red to match the interior)
Eibach Pro Springs, 20" Shelby CS69 wheels
SoS Triple pillar gauge pod w/ Aeroforce Interceptor gauges
GT-CS Side scoops
FRPP 4.10 Gears/ FRPP Hot Rod cam