I have a 2007 LS 460 built late in the model production year. I have been disappointed with the ride quality in many respects. I traded up from the ES hoping for that "silky smooth" and quiet ride that one expects in a car of the caliber of the LS. It's strange. On some road surfaces the ride is very good. But, on too many others, it is harsh/sharp (with the accompanying noise to go with it). In some respects the ES is better. In fact, I recently rented a Dodge Avenger when travelling and was surprised how often I noticed that it rode better (and quieter) than my LS would have under the same road conditions.
Some say the move to a stiffer suspension was to improve handling. Unfortunately, I don't think that was accomplished. My car still handles like a big car (body roll, etc.), but without the consistently smooth ride of one. Some credit the problem to the tires. They look good and help with the styling changes made to produce a better looking, sportier LS - much improved over its predecessors. I'm just sorry the ride suffered in producing the new look, which I really like.
As for the engine noise at idle, I have that problem also (diesel sound, knocking, tapping, clicking, etc.). See the thread on Intake Valve Noise. It seems that some LS 460 owners have never experience this problem; some have but it was corrected by application of the related Lexus Techical Service Bulletin; and others - like me - were told "It's normal; get used to it." I don't think it requires a move up to the 460L to get an engine that is quiet at low speeds and at idle, since many (most) 460s are fine - just not mine.
By the way, I'm not one of the "Lexus haters" who slip into this forum from time to time. I have driven a Lexus for years and love them. However, this latest one has not measured up to what I expected.