John,
Will you do me a favor and take pics of the door latch/lock mechanisms for me?
Read the comments on the thread about door handles, it will tell you how to service the handle mechanism.
I would wash out the inside bottom of the doors. As the wipers wear out you get debris building up in there that will retain water (esp when your Pig is PMS'ing!) and cause rust.
See if you can identify for me why my rear windows are so stinking hard to roll down! If I am not careful, the windows will pull out of the channels - bummer.
The window cranks can be removed by reaching behind and springing the little horseshoe clip behind them. AFAIK, you can still order the metal and plastic cranks from Toyota - see CDan.
Does this help?
Good luck!