ya you wont make much of a difference with stock replacement unless you do something called UPGRADING. also why would you waste your money changing your brakes when they don't need to be changed? especially the emergency brake pads, never herd of someone replacing them on any car unless they drove with the e-brake on.
as for your stereo get a cheap amp to power some good speakers and a good amp to power your sub.
upgrading your alt will need to happen at some point (depending on electrical demands). running 2 amps (or 3) you will exceed the output of the alt just running the stereo. (dimming headlights suck at night)