My guess is that the problem is in the head unit or amp. The problem could be in either. I had the right channel in my 00 LS cutting out last year and most people guessed that it was an amp problem. It turn out to be a bad connection at the balance control of the head unit. The problem was intermittent for several weeks before the right channel failed completely.
Is your system the standard Pioneer or the Nakamichi? Here is where I had my head unit repaired:
http://carstereohelp.com/ They have some basic diagnosis information for some Lexus radios on their website. BTW, their service was outstanding.
Have any friends with a similar GS? I figured out that my problem was the head unit by connecting my amp to someone else's Lexus.