Replacing radio / batteries' negative disconnected for how long?
 

I removed my passenger door panel to remove the door speaker on Friday. I have also removed one of the dash speakers. Before removing the door panel I disconnected the negative to the battery.

I needed to move the car, so I tied the door panel to the door reconnected the battery negative, and moved the car. It immediately started but with a clicking sound.

I disconnected the negative cable again yesterday. The driver's door window is too high for the door to shut.

I am going to likely replace the radio and amplifier this coming weekend. My question is can I leave the battery disconnected this long without problems?

Also what should I do to troubleshoot the clicking sound?

I recommend keeping a trickle charger on the battery to keep it maintained if you are keeping it disconnected for a long period of time. How old is the battery? The clicking sound is an indication of a weak battery. As for the windows... Those will have to be re-calibrated after you reconnect the battery, it's a simple matter of holding the button that raises and lowers the windows to the fully open then the fully closed positions.