I have seen mice get into things and their urine corrode stuff up real bad. I would check your under hood connections for voltage drops and pull out the relay bank and look for cooked or corroded wires. Like said above the grounds are usually the first place to start at the connection. Usually problems happen at the end points like the crimp terminals or switches. If multiple things are happening at once it sounds like a main feed wire or connection. These kind of problems must be found by measuring voltage drops or sometimes by wiggling the bad part will reproduce the problem.

It sounds like you have a bad connection and they can be intermittent. and then the battery and follow the wires checking volts from the start of the wire to the end point. If they look good, get a good volt meter and turn stuff on. They were able to get in one time and there aren't any stored codes, so it's destroying the evidence. The issue that the shop is having, is that when they plug the OBDII in during the flashing fits the OBDII loses power. I replaced the ignition switch and the shop did a load test on the battery and it's pretty much new. Usually if I let it sit for a while after the not starting fit, say.overnight, it will usually start up no problem. If this happens I know it will be doing the dash warning light flashing and won't start again. Sometimes if I hit the auto window switch up, and the window is already up, I lose power for a second, there is a loud beep and the headlights turn off. When it's running, it runs perfect (I get 47mpg). It works like this for both keys so they both aren't bad. If one key fob doesn't work sometimes I can start it with the other. Now, if you grab another set of keys it might start right up, or not. If you turn the engine over, no crank, just a clicking under the dash and everything flickers and the clock and trip meter reset themselves. The fuel pump in the tank won't fire and the glow plug indicator won't pop up. When starting, hot or cold, sometimes the dash warning lights will all come on.

Well, it was, they just called and said they don't know what to do, it needs an auto electrician. My 04 Jetta BEW TDI manual sedan with 157,000 is in the shop for a starting issue.

Jetta mk4