I have a 07 IS350. I had the same problem but Bay Ridge Lexus couldn't find out the problem. Took it to Queens Lexus and they told me it wasn't covered under warranty. Now I'm out of warranty. Been driving without any sound for years. $2,000 sound pretty expensive.

 

I would give Lexus corporate a call. Did you first have this problem while the car was under warranty? Or under the Lexus CPO warranty?

Though it wouldn't be covered under the CPO, Lexus might help you out when it comes to the repair costs; other manufacturers have with me, in the past. I had a VW Jetta and its roof liner started to fall. It was then 6 months out of warranty and under CPO and when I gave VW of America a call they paid for the part and I paid for labor.

Also, if your dealer is telling you the entire head unit needs to be replaced they may be mistaken. Though that would be a $2,000 repair, it is likely they only need to replace the amplifier which will be markedly cheaper!

Good luck