Just an off the wall suggestion............when you put the battery back on, and the flashing starts, I take it that you can't silence it with either the unlock key or the panic button ?
just behind the CL pump, tucked away, and bolted to the frame, is the alarm module. Try disconnecting that, although I'm not sure if the CL will work then.
There is also a fuse that controls the alarm, but again the CL will not work if it's removed. These are things I tried before realizing my pump was dead. However mine had a foot of water in the trunk, and the pump was well wet.