Sounds like you are going to make quite the system there.
Since <some> seem hesitant about the JL 13", I'll post up some alternatives.
DB Drive actually makes decent products. its a new company, most likely out of China; but they are probably making some decent stuff for what I can tell, and for good prices. The company has won several DB and SQL competitions recently. They make a 12" woofer that is shallow-mount and you can check it out here:
db Drive
Another shallow mount is Pioneer; for which I am partial to because I own a shallow 10". They are about 3" mounting depth in both 10" and 12" form; meaning you can likely keep your spare tire.
Pioneer USA - Home. My little 10" flat piston Pioneer is currently stuffed into a .2cu sealed box - it barely fits the magnet - and sounds beautiful; sacraficing sound efficiency in favor of trunk space. Its actually embarassed a few systems.
As for Pioneer, if you like the stuff you can get it all from Amazon and use a 30% off coupon I posted several days back. The Amazon coupon code for Pioneer discounts is VRCBKCX6. Im not sure if its still active...
Dont use rear speakers.
Also, the Metra Axxess works well enough; I posted some procedures here if you care to take a look.
Get the Axxess ASWC working - All buttons
As for amps, well; I am partial for the old Class AB circa 1990s. You can probably pick up some Hifonics (Made by Zed), Orion HCCA, or Precision power Art or Powerclass series for the same or even less than cheap new amps today. Ive actually found that these old amps are selling for dimes on the dollar of what they used to be worth; meanig you can get a $500 amp from the 90s for less than $100. I got a PPI PC2150 (150x2 rms at 4ohms) for $80 off Craigslist; this amp costed $600 brand new; and they sound phonomenally good and clean at the cost of drawing more power.