I'm getting a used amp, it should hopefully be here this week, I will post back here when I replace it to finish up this post. Have you tried disconnecting the Lexus Link system and all that? If so it is likely the amp, especially since it is an 01, from what I understand, all the 01's had an issue with the amp, I guess some last/lasted longer than others. I'll let you know.
FYI
The 01 ml amp part number was 86280-0w040 stay away from these on ebay
The 02 part number is 86280-0w041
Lexus apparently removes the part numbers for defective parts and updates it by adding numbers to the end of it, hence the reason why it ends with 41 now.
The documented "Lexus" refurbished 01 amps that end in 0 have a small sticker on the side by the fan, the number on that sticker would be higher than 74xx
The 01-03 amps are the same.
The 04 and newer are different and aren't compatible.