I've experienced this same issue multiple times. Can't fully explain it, electrical is not my strong point, but when the clutch is engaged, it enables the clutch switch used for the cruise control (basically like an inhibitor switch on an automatic but only used to disengage the cruise control if the clutch is depressed on a manual). I can't remember if it closes the circuit or opens it when the switch is engaged. Anyways, I've noticed that the idle is absolutely affected depending on when the clutch is depressed or not. How and why...I don't know but it is I proved it by pulling the switch off the pedal and depressing it by hand. How I fix this is to rerun the TSC/ISC reset procedure until it resolves the issue. Basically, depress the switch and run the TSC/ISC and set the idle accordingly. Then see how it runs after the switch is let go. Tweaking the idle settings between the two. For a quick fix if you don't use cruise, unplug the switch and see how it runs (or connect the leads depending on the 'normal operation'...like I said, I can't remember if the circuit is normally open or closed when the clutch pedal isn't engaged).
As much as I love these cars, I hate our engine management systems especially anything pertaining to idle. I've done the TSC/ISC reset over 20 times on a single day until I got it to be somewhat what I wanted it to be during all operating conditions...and it still goes erratic at times but won't stall.