Most I have seen have yelow paint on the throttle stop locking nut. Good point about the CTS (closed throttle switch) I'd check that is working/check wiring to it. I've seen test/set up somewhere posted by rubjonny. Only other thing as this is a conversion not a 'factory' 16v any chance the plug for the ISV is on the wrong thing (might not be possible but an idea)
Okay, so after more fiddling i think i may have found the problem, my idle control unit is slightly different, the number on it is 447 907 393 B i think it is from a early kjet audi, but im betting this is what has been causing the issue. So now i need to find an actual kr unit to test my theory.