's subroutine creates a constant effect. The additional "End the run" subroutine added by it is there as soon as the next ice is encountered because this effect is always on and doesn't trigger or resolve. As such, the additional subroutine will be present when 's ability triggers to bypass the ice.
If the Runner encounters a after Sensei, then the "End the run" subroutine is located after the subroutines Komainu gains by itself.
Suppose the runner encounters Sensei and does not break the subroutine, and then encounters , which has been chosen as the target of Femme Fatale. Does it cost 1 credit to bypass Ice Wall with Femme Fatale (because these are simultaneous conditional abilities, and the runner may trigger Femme Fatale before Ice Wall gains a subroutine), or 2 credits (because 'for the remainder of this run, each piece of ice encountered except Sensei gains "End the run" after all its other subroutines' is a constant ability)?
If the previous answer is 2 credits, then suppose instead the runner encounters Sensei and does not break the subroutine, and then encounters Komainu. Does the end-the-run subroutine come first, because it is already present, as the first subroutine, when Komainu gains its net damage subroutines, or last, because Sensei says the end-the-run is after all other subroutines? Or something else entirely?
Subroutines gained by a piece of ice's own abilities have higher priority than subroutines given to it by other card effects that say "after all its other subroutines."