Replacing radio / batteries' negative disconnected for how long?

[Parker986]

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?