all those look great. one thing to mention (at least in my opinion) is the rears are not really needed. the size of the cabin works great with just door speakers and tweeters.
as far as a sub goes look for one in a truck box, most of the single sub truck boxes will fit behind either seat comfortably (as will both ttops)
you mentioned replacing the stock sub and thats what i went with. not sure about putting one in the stock location, never done it
also if you havnt already found this GREAT resource check it out
MKII Toyota MR2 Audio How-To
personal tip - remove all 3 of the factory amps if you have a model with the premium sound (located where the seat belts go on both sides) and run ALL NEW WIRES, power,ground speakers, etc. makes a huge difference for cheap and you dont have to deal with toyotas wiring job.
good luck!