It sounds to me like your HWH pump motor quit. I've had it happen while putting the gen slide out for fueling. Luckily, mine went out about 6 - 8" before quitting. It's very possible that your battery problem took a toll on the pump motor.
The only way to know for sure is to use a voltmeter to monitor the terminal of the pump motor for 12+ volts. If you read good voltage on the pump motor when pressing the extend switch but it's not running, then it's bad. It self grounds internally so there's only 1 - terminal with a large red cable attached. Some folks have reported that tapping the motor with a hammer can sometimes get it to come to life temporarily.
If you don't have any voltage on the pump motor, then you could have a bad solenoid relay. There are typically 2 - solenoids strapped to the motor. The left solenoid (based upon my '03 configuration) is the main pump relay and operates for all HWH operations EXCEPT the gen slide. There should be a solenoid to the right which is dedicated to the gen slide. I've also had this solenoid short out thus blowing the fuse that feeds the console. Since you're hearing "clicks", the fuse should be OK.
Theoretically, if the gen solenoid is bad then the jacks and slides would still work. Since they don't I'll be surprised if your pump motor is not the problem. I've gone through 3 since owning my '03 and I'm not the original owner. Maintaining the very best voltage to the HWH system is important to longer pump motor life.