1) check error codes
2) check TPS voltage (i know you have manually, but that wont tell you if ECU is getting that signal)
3) check 'Closed Throttle' switch and ensure its on(closed) when throttle closed and open when its not
4) check AAC value is fairly low (<30) on warm idle
5) check coolant temp sensor starts at air temp when cold, and warms up correctly with motor
6) watch ECU ignition timing at idle - generally if the ECU thinks the car is idling too high it will lower timing - but some people with high idle issues etc will see timing is solid at 15deg, and combined with closed throttle switch saying throttle is open, made ECU think it wasnt 'idling' hence it didnt keep idle low.
7) check actual timing via the base idle/timing mode to lock the adjustments (otherwise timing moves all over the place), and see that its correct with a timing gun
8) check other switches/sensors to see what changes when you put the clutch in if this affects idle
im sure theres more things that could be tested, but thatd be a start.