Welcome to the club.. Sounds like you got a pretty good deal.
Your LS should have had a timing belt replaced at 90K. That would be the biggest issue I would research. If it has not been replaced you should have it done.
Your taillight addition will get mixed reviews on this forum.. Just remember it is YOUR LS and it does not matter what other people think.. If you like it, that's all that matters. You will absolutely love this car.. Have fun with it. Like the commercial says.. "When you turn your car on, does it return the favor" and the answer is "Why Yes it does"
Of course that is not a Lexus commercial but it should have been..
In regards to your speakers, you can replace them with after market.. Look at crutchfield.com and see what they have to offer.