You say no to JL, but say yes to Skar? Ugh...Kicker and JL actually have a line of fantastic products, sure you can obtain similar no problem, but please don't go and tell someone to look into Skar. At the very least recommend Sundown SA series or Obsidian OA series over Skar garbage. Also, if a fellow can find for instance some 12w6s or 12/13W7s, for a decent price, and/or say a Kicker _ _2500, then go for it. I would love to have a pair of Kicker's ZX2500s to replace my ol' Cactus 5k to change things up. And for a FANTASTIC balance of SQ and SPL, there isn't a single driver on the market (yet, but Jacob is closing in on that one //content.invisioncic.com/y282845/emoticons/biggrin.gif.d71a5d36fcbab170f2364c9f2e3946cb.gif), that outperforms the W7 line.
Anyhow, my recommendations would be a 4ch amplifier of say PPI Phantom series and a decent set of components up front. You can get away with spending less than $200 for a lovely set. Be sure to obtain the speaker spacers or make some, because our stupid Rexes have like 2-2/3" of mouting depth for speakers up front lol. AGH! I hate that fact about our Scoobs.
Then a decent Class D monoblock amplifier. Depending on how "loud" you want to go, and how much power you want to run, a single matching PPI amplifier could be had for fairly inexpensive, then just add another when you want to go bigger. IIRC they have a nice 900Wrms or 1kWrms amplifier. Then, purchase some plans, or have somebody like myself and a bunch of others on the forums design and build you a proper enclosure for your woofers. That enclosure will play a HUGE portion in it all.
It would be a great idea to deaden a bit and moreover seal up those front doors, so your components can REALLY shine as well. Proper cabling is a must also. Depending on how much power you want to run in the end will decide whether or not you will need an alternator upgrade or not. The stock battery up front a quality "audio" type of battery in the rear will be enough to support lots 'o power just fine. If you want to runs lots of power, there are plenty of options out there for amplifiers as well, that are great quality and efficient. It just depends which woofers/power handling/what your entire goals in the end are. Seeing as how a properly done 1kW to 1.5kW can make tons of people bail out of a car, it all depends what you want.
You do not need to spend nearly the $2.5k you were thinking. Not even close. You could have a stupidly powerful and clean system for less than half of that I assure you.