The kicker sub/amp combo would probably work, BUT, the sub is made for 0.33 cu t., and the stock enclosure (on 95-01's) is slightly larger. The kicker sub is also incredibly inefficient, at just over 82 dB. $130 for the sub and $130 for the amp is kind of a lot of dough there, you can get a better setup for that money.
For a budget build with the stock enclosure, I'd suggest a sub like the 8" shallow Premiers or the new Kenwood eXcelons (around $99), or the 8" JBL GTO which is under $100. The Premier/eXcelons will give decent but not pounding bass, the JBL GTO's (which get my personal recommendation even though they are now made in China, the good ones were made in the USA until recently) have some good punch for a little sub IF you pair them with a 200W RMS @ 4 ohm amp.
If you won't be happy with just decent bass, you can save yourself the money in the long run and either get the 10" JL stealthbox or custom build your own, or have a shop build you something. You'll save money in the long run by not wasting it on a budget setup and being unhappy with it, then trying to get rid of everything and start over again.
The 10" Q-logic stealthbox is also an option, it's smaller than the JL stealthbox, but techieman's getting rid of stuff for pretty cheap so you may want to hop on that deal for some compact bass. You'll have to rely on his input as to how hard that enclosure/sub/amp combo hit in his ride.
As for the budget setups, a sealed enclosure is a sealed enclosure. Sure, the stock box may have some flex that something made out of 3/4 MDF doesn't, but the stock box is waterproof, not to mention lighter. Just about any sub that needs a 0.35 cu ft/ airspace and doesn't require a ton of power will probably work great in it. The limiting factor is more the subs that will fit in the enclosure than the enclosure itself.