Off a quick search and from my head;
Resonant Engineering, Digital Designs, JL Audio, Rainbow, Dynaudio, Focal, Image Dynamics, Morel, and Zapco. These are all companies that make great speakers, but can be a little pricey.
Some of those companies also make amps. I know from personal experience or experiences of friends that JL Audio and Zapco make great amps. The Alpine PDX amps are good for powering multiple speakers, just check that they put enough power out for your speakers of choice. Overhead is always good, don't skimp on power.
For subs, Resonant Engineering, Image Dynamics, Rainbow, and JL Audio are all supposed to be good. I haven't heard subs from RE, ID, or Rainbow, but I can say that the JL Audio W7 subwoofers are incredible.
With $4000, you should be able to afford pretty high quality stuff. How much is the store charging you for install (estimate)? Are you buying the equipment online or from a B&M?