Check to see if you have power to the master relay - the big red cable coming from the battery to the relay. If not, it's probably related to your battery hookup as you suspect. The control board gets 12v from the ignition switch as well which will light up your control board lights, but not let your pump work or the solenoids.
If the cable to your master relay is hot, check all grounds, especially the mounting bolts on the bottom of the jack system that mount it to the frame. Also, check that the nut on the ground post where all the white wires connect is tight.
Here's a troubleshooting guide if your jacks are 625 series:
http://www.hwh.com/ml35963.pdf