6.5 DO fit in doors it only takes a very slight bit of mod to the port and even the grills fit flush, ive done it on two cars. JL audio type speakers used. also, MB quarts will fit as well, you cant just drop em in but like i said a slight bit of mod to the port diameter and its a factory look as neat as OEM.
as for the factory amp toss it with the factory speakers. depending upon what you paln on using, a 300x4 would suffice but i would recommend two sep amps one driving the sub by itself. as for subs, JL audio 6W0 will fit like factory in the rear bulkhead, just remember to enclose it wll with silicone/fiberglass so as to tighten up that hit. or, an easier way; make a rear bulkhead panel custom fiberglass mold (the entire thing) and do so with either a 8" or 10" sub capacity port, an 8" cap port will only extend out into cockpit aprox 3/4" more than OEM so its not even noticable and the sound is without a doubt superior. many still liek to passenger footwell, me; nah too ghetto and i like a stealth system, one that loooks liek it came with the bucket until you turn it up and then everyone knows it aint stock, LOL
also, FWIW; remove spare tire and custom the trunk, easy place to get creative to mount the amp(s) and crossovers
i put the head units brains and also I mounted a 40gig hardrive under the seats.