The alarm is a GE Security part No: 60-806 60-806-95R. I have disconnected the battery in the main box and disconnected the phone. I still get beeping. Can you help?

You say you have disconnected the battery. Have you also disconnected the AC power? Are smoke detectors installed as part of the alarm system?
Do you have a user's manual?

No is that the first two wires that attach to the screws in the large box?
There is one smoke detector that is part and it's hard wired. We are no longer able to get the make so my husband replaced it with another brand that is also hard wired but it is for smoke and carbon monoxide.
We don't have a user manual but I did print out the information for installing the system.