I know these LS's can be a pain from what I read. Thankfully I've had minimal problems with my '04 and it's just about to roll 67K. However, one thing I do notice is the transmission.
You all talk about a "hesitation" in between 40-60mph, and most of the time I see that this is chalked up to COPs and spark plugs. It seems as though when these are replaced the problem still exists (sometimes). I would like to recommend your valve body solenoid in your transmission. I have this problem with my LS, but it only happens once in a blue moon. I've worked on my fair share of cars and diagnosed them. I'm not a mechanic, but experience speaks wonders. To me, it honestly doesn't feel like an engine misfire.
In a similar situation with an older car of mine (though it happened on a much more frequent basis and to a larger degree), I had this "stutter" problem. For the life of me, I could not figure it out. Eventually, after I exhausted every possibility, I told myself the only thing it could be is either the valve body solenoid, or the transducer that goes along with the solenoid. I took a gamble and replaced only the solenoid, and sure enough, problem solved.
I'm still trying to figure out what solenoids need to be replaced in this transmission (I know A, B, and C typically go bad). My transmission doesn't give me any grief for the most part. Just on random days there might be a slight delay in the 2-3 shift and ever-so-often the 3-4 shift. And then of course there is the small hesitation at about 50 - 60 mph under slight acceleration, typically after coasting for whatever reason. Again, might be a valve body solenoid.
Just a thought to add to your list of things to maybe replaced should any of you be so inclined. Sorry for the lengthy response, just wanted to explain thoroughly.
CJ
