Nothing jumps out as clearly wrong (besides the rain sensor being connected to commons), what does the ohm meter read when measuring between zone 2 (brown) wire and what looks like the second red common from the left (that is the common that looks like it belongs to the same brown cable bundle).
It may be that some residue is left on the wire from the black electrical tape of the original rat nest. You may wish to clean the end with alcohol to make sure that the proper connection is being made.
While on the subject, disconnect the white cable from the right most common terminal and follow it to the brown cable. Than follow the red wire that comes from the same brown cable (it looks like it is connected to the leftmost common terminal) and disconnect it as well.
Connect these two cables to the S1 and 24 - terminals to make the rain sensor readings possible (rain sensor would need to be enabled within software after the right hookups are done).