Ok I looked at the car briefly, that rear little hard line from the earlier diagram is welded to the same mount as the evap line, so I guess it stays. I located "C" and "E" physically. E is actually a T-connection off of a nearby heater line, and C is over near the back of the engine block. I also looked around elsewhere in the service manual, and found this (red C/E marks from me):
Looks to me like C+E don't even need a bypass connection. One could simply cap them off right there and be done with it, as the throttle body coolant path is independent of everything else. So now it looks like remove the 4 soft hoses, put crappy dust caps on the 4 throttle body connections and the 2 sides of the tiny rear hard line, and then put 2 good cap-offs (as in, must prevent leak of hot coolant) at points C and E.