Subwoofer would be the least of my concerns. You can get a solid sounding sub for around 150. For amplification Id go with the Arc KS300.4. Its fairly compact, puts out rated power and can drive your whole setup.You would feed 90 a side to your components and 350 to a single 4 ohm sub. Id try to portion a good chunk of your budget toward your component set since theyre responsible for 90% of the frequency reproduction.
Find a local Morel dealer and check out the tempo 6 for a solid budget set. As far as a head unit, just find one that has the options you need. If you dont need a touchscreen theres a ton of options. If you do need one then expand your budget a grand
This is just one option, hope it helps.