I've got the same exact symtoms on my 97 LS400 with 175k on it. Have you ever checked the fuel pressure? You did have a "gunky" filter right? So this in turn would cause the fuel pump to work a lot harder and cause it to fail sooner. I haven't checked my pressure yet, but that is the first thing I'll do as soon as I find an adapter to the fuel rail. My car had a CEL on and the codes were P0300 random misfire, p0302, p0304, p0306, p0308 Cyl 2,4,6,8 misfires and also a Bank1 system too lean. Now this shows me that the engine either doesn't have enough fuel or I have an intake leak. Now I removed the vacuum line off of the fuel pressure regulator and this should increase the fuel pressure and make the engine run rich, But I noticed no change. Most cars you will notice either an increase in RPM's or chugging because it is running rich. The next thing I tried was to pinch the return fuel line. This would dramatically increase the fuel pressure to 60 to 80 psi, so you only do this for a couple seconds at most to check pressure or engine change otherwise you could damage the fuel pump. So when I did this there also was no change in engine idle. So my next step is to check fuel pressure and confirm my theories. The only part that does not fit into my theory is that the problem happens when the engine idles for a long time and warms up. This makes me think of an intake leak, but I'll test the fuel pressure first, and when that is good then I'll look into others.
I read all you posts and noticed you replaced a lot of parts. How much did all those parts cost you? Are they all new parts or just more used parts that are possibly bad as well? Did you test all these parts before you replaced them or are you just shotguning parts at this?