good grief! Gotta admire the persistence there. Your previous owner seemed to think he had better ideas then Toyota and did it with a lot of wire. A couple of thoughts. Since adding aftermarket stereo is trivial with a proper harness I would trace anything that goes to the center dash and is connected to the new stereo and then pull it. Hoping the previous person left the exisitng plugs so you can fix that section pretty easily. Your reall issue is the alarm. Messing that up may kill the ability to start and you said you are not expereinced with electrical. I would look at paying a local alarm shop to undo it - that way you have some fallback if they screw it up. I would not touch that without a Toyota wiring diagram and a diagram for the alarm