My 90' also idles at 300-400 rpm, adjusting the air bypass doesn't affect my idle either way. Since every sensor and output device is new and my TPS is adjusted correctly, I think its more of a computer issue/calibration type of thing. Mine also does not die or stall but I'm not having any knock/ping like you are having. Here is a list of whats new on mine.
block/head-newly rebuilt
Intake and TB cleaned with ultrasonic cleaner
injectors
distributer
TPS
CPS
MAT
CTS
MAP
IAC
O2
new cat
EGR and solonoid
fuel pressure reg.
fuel pump/pickup screen/fuel filter
knock sensor
cap/rotor/NGK plugs/OEM wires
NSS has been cleaned
all relays
All connectors under the hood and dash have been pulled apart and cleaned with die-electric grease added.
Cleaned all grounds, and added a battery- to chassis ground from the side post on my OPTIMA.
No change in my idle, it sounds like a old John Deere tractor. The idle kicks up when the AC is on to maybe 500 rpm. I'm getting great mileage and the power is unreal. It runs much better/stronger than my other 3 HO XJ's.
I've decided to live with what ever the low idle issue is.