I have a harbor breeze ceiling fan. Coming from the ceiling are white wires, green ground wires, and two black wires (one controls fan and one the light). Coming from the fan are a blue for light, a black for fan, a green ground, and a white for neutral.

One black when connected to either the fan or light wire will work them (I tried both). The other black does not seem to control anything. Also, I seem to have lost the connection between the wall switch and the fan or light as all that will turn them on is the pull chains.

I need some guidance

Sounds like you have a switch loop. Does one set of white/black from from the direction of the switch, the other from some other direction? Are any of the whites marked with black?

Ceiling fan wiring - Ceiling Fans N More (http://www.ceiling-fans-n-more.com/ceiling-fan-wiring.php)