First of all Jay, Welcome to you and your wife to the LOC! We're glad your in the club and look forward to your contributions and questions.
As Jim asked re; the CD changer, are their cd's in it?... will they eject? Can you put a disk in it. The reason we ask is that some of the earlier changers after about ten years or more start to act up for some reason and the changing mechanism jams a lot. But usually they will play. For the them not to play means that either the disk is not spinning, the laser reader has gone south, or the preamp/circuits are bad. If the radio works, which it must since you talk about the speaker sounding bad, then it's not the amplifier which is the amp for all units, radio,CD, & tape. If you will do a search of this board/site you should find information on taking out the dash and unit. Since you are a new member you can not yet PM (personal message) anyone yet. I will leave a note for "dcfish" the sites approved Lexus audio equipment vendor, just in case you need his expertise. I think it's after 5-10 posting, you get privileges to begin PMing other members.
The Levinson speaker is a unique design in that it's impedance is other than what is normal for Car audio use. Most car audio is 4 ohms, while this particular year/model is probably 8 ohms. (don't hold me to that). If it is the speaker and not something else like a crossover, try ebay and make sure it is for the Mark Levinson. You want to enjoy the full richness of the system.
Look for the struts as well while your on line or go to Sewellparts.com . This is a Lexus dealer in Dallas, TX that we have an arrangement with for LOC members. When you register, tell them your a Lexus Owner Club member and get a hefty discount on parts and accessories.
For the roof and how to replace the speaker, again do a search first and see what you find.
Let us know how you come out.
Merry Christmas,
Paul