THIS IS THE MOST ANNOYING THING EVER. I have looked ALL over for answers and there are a few people on the LExtreme.com type forums all looking for a definite answer to this problem. The problem? Yeah there are lots of instances of this model of car stuttering at cruising speed. They accelerate just fine when you punch it but if you just give it half throttle or less the car will act like it's misfiring.
Here is a post that I posted a couple of weeks ago:
I was invited to help a local mechanic shop troubleshoot an LS400 today and I worked on it for about 2.5 hours swapping out more parts and checking things over. Still the same symptoms as you have described. Very annoying and checking the mechanics database there are A LOT of other mechanics that have had the same problems!
It must be a wiring fault but I'll also be checking on that TPS the next time I give it another session. There is a LOT of heat in those stock LS400 engine compartments and it must just wreck the wiring. I know that almost any clip you decide to remove must be done with extreme care since all of the plastic breaks when you apply force to disassemble things.
Not fun but I'm pretty determined to help the poor soul that owns the car. 
Or maybe I should tell him it's a lost cause and offer him 500 bucks...