So after searching "amplifier", "mark levinson", and "subwoofer"...reading about 30-40 threads about the factory system and adding an aftermarket amplifier/sub I learned one thing......that I still dont know jack **** about this system.
I have no problem changing a valvespring or replacing an evaporator, but this system seems to damn complex.
I have 2 tweeters out, one going bad, and a bad factory subwoofer. Even with my discount being that I work in Toyota parts, it's still just under $1000 to fix these .

I want to put my Kicker 12 that i have lying around, but my previous LS430, had the amp short after about a year of ownership.
Am I ranting....yes, a bit.... but basically, either I pay $1000 and have a subwoofer that will almost inevitably fail again, or I pay $100 to install my aftermarket subwoofer and have that fry the amplifier after a while.

 

There are options to get you back up and running, but it won't give the punch that an aftermarket amp and sub would give you. I installed a 50 dollar JL Audio sub, and it's been sounding great for over a year. I do not, however run the amp at high output levels. So I'm not endangering the amp..