Thanks for the tip. I just talked to the leak specialist, he said $160-250 on average. Considering I saw references to $3400 to have stuff like this fixed at the Lexus dealer, including having the carpet replaced, I do not mind paying somebody 2 bills to identify what the source of the leak really is and prevent more extensive damage than I'm already facing.
Also, I found the technical manuals here in the forums for the '99 RX 300 and from what I can tell the sound system is close enough to '00 that I can use the troubleshooting procedures in the body electrical manual to find the culprit with the stereo problem. Given what I already know and have checked already, I suspect it is the power amplifier got wet or a wire harness connector is shorting to ground due to being wet.