I suspect one of two things.
First, somebody has messed with the idle stop screw on the main butterfly to "fix" and idle problem caused by a bad ISC in the past, raising the mechanical base idle speed, in which case you have to do the fsm base idle speed setting they say is not necessary (so why do they tell you how?). This is fairly complicated, and also requires resetting the TPS/IPS so it reads proper throttle idle position and open position.
Second, you have a vacuum leak beyond the capability of the ISC to compensate. Look for it by sound on an idling engine using a piece of vac hose in your ear. You can hear the hiss easy that way, and localize it. Scan the end of the hose around (it's very directional) and you'll home in on the source.
There is also an air bypass screw on the top of the TB, perhaps under a cover, down in a hole. Try adjusting that to curb idle speed after warm up. Since that's the easiest, I might try it first.
So I have fiddled with the air bypass screw; I've tightened it as much as possible to get the idle as low as it will allow, so I don't think there's any more to be done there.
On the vacuum leak question, where exactly should I be looking? There aren't very many vacuum hoses on this thing (brake booster, fuel pressure regulator and evap canister, from what I can tell) and I've replaced those except for the brake booster. I assume that any leak of interest would be downstream from the throttle body? The only other places I can think of would be the gaskets, i.e. TB <-> plenum <-> intake manifold <-> heads. Those are all new too, of course (the gaskets).
I'm saving the adjustment of the base idle for last. I can't swear that that screw has never been tampered with, but I know that I've never messed with it.
thanks,
steve