I followed the ion pod discussion and absolutely concur with blssdwlf but I'm unable to do so here.
A) The whole purpose of the events we are discussing is to retake helm and navigational control from the M-5 computer by "disrupting" the automatic helm navigation circuit relays from engineering level three. How do you "disrupt"? Very likely by withdrawing the power feed from the automatic helm navigation circuit as without power the circuit is as dead as the Dodo and M-5 can't use it any longer to steer the ship.
B) After their sabotage they find out they did not regain control and Spock asks Chekov to examine the "H279 elements" and the "G95 systems" which he does at the bridge's engineering station (navigational systems and "Ass't Navigator" are on the other side of the bridge according to the official bridge station layout!). The H279 elements seem to be okay, but the G95 systems are dead (no indicator).
C) Scotty than expresses disbelief as the primary system seemed "active" (i.e. powered by energy) but actually wasn't. They were under the impression of re-routing and re-connecting active power feeds while in the meantime the M-5 computer had already done that on its behalf, anticipating their actions.
I suggest to take another and unbiased look at the screen readout and the schematics ("Eng 6") http://tap364.webs.com/engineeringstation.htm
While Troy Palmer admits that he made up the text on this engineering display (there's no close-up shot of the original prop, yet) the schematic clearly suggests we are looking at pressurized containers / bottles of some kind and not
some kind of circuit diagram exclusively.
The only reason I introduced this diagram into the debate was that it appears to me that on the left side we are looking at the three matter-antimatter reactors (the two from the nacelles and the smaller one in the engineering hull) with only two dilithium crystal conversion points beetween the three and the power flow (green) emmanating from these.
I really don't want to sound sarcastic, but if it walks like a duck, quacks like a duck and looks like a duck, it probably isn't a wild goose.