Electrical Gremlins in ignition and the doors!

My 2000 C2 Cab is having some crazy electrical issues that make driving the car and parking it anywhere a bit of a crap-shoot. I've changed the ignition module that sits at the back of the ignition stem, but that did not fix the problem. I have searched and read on several of these issues individually, but nothing comes up that would tie them together. Symptoms: 1) My car came with an aftermarket Sony radio that does not turn off when the car is turned off. Doesn't matter if I pull the key or not, I have to turn it off by popping off the face plate. 2) Interior door lights stay on when I remove the key from the ignition. 3) If I leave the key out of the ignition for more than a few minutes, there is a good chance I will come back to discover the windows rolled down and the interior lights are not working at all. The ignition will turn over the starter (voltage gauge shows 12v). Lights is the dash come alive, but the car doesn't start. If I mess with the key a bit. Usually, if I wait a bit and mess with the key in the ignition, pulling key out, putting it back in an turning it a few times, the car will eventually honk at me, the interior door lights turn on again on, and fire up. 4) Passenger door does not lock at all. 5) Windows don't drop 10mm when doors are opened. This is a more recent development since I started trouble shooting the clamshell. 6) Convertible top does not actuate from key remorte, nor from turning the key in the driver door look. (could 1-5 all be related?) 7) Clam Shell mechanism does not work at all. Top hydraulics work, as do the side winglets. (Separate Issue) Again, I tried replacing the small part at the end of the ignition stem which seems to cause quite a few wonky electrical quirks, but that did not help. It seems to me there might be multiple microswitches, relays or other component contributing to this problem. For starters, I have ordered a replacement passenger door mechanism, but I am not necessarily convinced that is the problem. Have any of you been faced with these issues before?

What is the part number of the electrical portion of the ignition switch that you replaced? Meaning - did you get an EBay switch (el cheapo) or the more expensive switch ($30)? Most of the problems you refer to could be traced back to the ignition switch.

I bought the cheapo version... part number is: 4B0 905 849

I don't think it's the switch. But if you got the cheap ($8) switch you'll be replacing that again soon anyway. The $30 or so switch is the one to get even though it looks and (nominally) functions the same. Order it and keep it in the glovebox with the necessary tools. I've had both and while the $8 one didn't last very long it never caused any ancillary issues like what you are experiencing. I have no idea what the problem is with you car but it could be battery related, i.e. a weak battery tends to cause all kinds of issues. Others will have more info and suggestions, no doubt.

Had my indy hook up his code reader... Alarm system is returning 10 different codes. Everything malfunctioning seems to interact with the alarm system. We both believe the immobilizer got wet at some point in the past. More to come later.

Was the car in a flood? If not....are you 100% sure of this?

The windows not dropping when the handle is lifted is probably due to disconnecting the battery at some point. Roll the windows to the fully up position, and then press and hold the "up" button for the driver for 10 full seconds. Do the same for the passenger button. The window limit will now be set, and the drop functionality will be restored. This COULD be preventing the automatic drop functionality (assuming this used to work before but stopped at the same time the windows stopped dropping).

Quotes source posts: 13598320, 13597948

I've only had the car a couple of months, and I did disconnect the battery while I was replacing the rear window regulators (PITA, but rewarding DIY). Do I need to do this with the engine on, or off? If off, key in ACC on position? Could have been... If water damaged, I hope it was just a case of clogged drains (which seem to be pretty clear now) or the PO left the roof open and it got rained on pretty bad. The car is in the garage and is our 3rd car, so it's not super-urgent. I can drive it on little fun trips as long as I don't have to park the car for long and remove the key. At this point, I'm leaning towards extracting the ECU & Immobilizer and mailing them (along with my key) to Specialized ECU Repair in Ft. Lauderdale for evaluation next week. If it is indeed the immobilizer, that's a $775 experience. I found out along the way that they can also program keys, and since I only have one key for this car I figured I'll try my luck in the remote programming lottery and I ordered one of these to send along. This will also buy me time to figure out this is the best and most cost-effective way to fix my issue: http://www.ebay.com/itm/142110821034?_trksid=p2057872.m2749.l2649&ssPageName=STRK%3AMEBIDX%3AIT

Okay... so I decided not to pull my ECU & Immobilizer and mail them (along with key) to Specialized ECU Repair in Miami. After discussing with them at length, it appears that there was a chance they would end up having to charge me for a key as well. I was looking at about the same price I was quoted from the local dealer. Plus, I needed some expert diagnosis on why my sunroof clamshell was not working properly. After multiple manual open/close sessions, I was pretty sure I was going to have to have the top calibrated/re-synchronized... So, off the dealer the car went. The immobilizer did fix all of my electrical gremlins, and the clamshell lock started to work properly as well. A secondary issue with the roof turned out to be the driver side winglet was not moving as freely as it should. Some lubrication on that part fixed my roof issue. Car runs fantastic, doors/locks/widows/tops/central locking/security system are working as they should. The dealer was able to make my new second key open and start the car, but the second key remote part does not work. Still, this at least gives a 2nd key for the car... One thing the dealer service manager did not know to tell me, and didn't realize... was that they could not use the pre-owned immobilizer (so I had to pay for a new one) and that they could not use my old key remote (so I had to buy a new one of those too). Due to me being a new customer and some mis-communications presented to me by the youngish service manager at the dealer, they comped me several hours of labor without me having to get bent out of shape... and they got me out the door for under $1k. It was still a few hundred more than anticipated, but well below the $1600 on the original invoice. Had I sent the bits to ECU repair I might have saved a couple hundred $$$, but I would still be clueless about exactly why my cabriolet was out of sync and would be spending time and more money dealing with that issue. No regrets... At the stage I was in the overall project I took on to make this a sorted 911 that I can drive with solid peace-of-mind, I think that was the right thing to do. My family and I are loving the car. I can live with the way things went down.