how much space do you have? or are willing to give up? Most brands have subs that will work very well in as little as .6 cuft(net) sealed, like the Alpine type R 10", my type R 12's are in .8cubes each and sound great. Since you're keeping the rest factory, you won't need a "killer" sub set up (you also mentioned SQ ), so go with something that needs 200-300watts and works well in a small sealed enclosure. It should not overpower your factory system. Check out Boston Acoustics, JL, Image Dynamics, Alpine, MTX, etc...

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2004 300M SPECIAL
Alpine CDA 9833
Alpine Pxa-h701
Alpine Rux-c701
Rockford fosgate p400-4
Rockford fosgate p4004
Hifonics BX 1205D
JBL c608 GTi
JBL p963
Infinity 2.5" center channel
Alpine type R 12"(2)
200 amp alternator
yellow top battery
0 awg power and ground (welding cable) 300 amp anl fuse
all active SQL set up with 2000 watts rms