So, got some tips for you, having just finished recording a test run for Iji through the Pacifist route:
http://www.youtube.com/watch?v=pNYWXWA_Vl8&feature=related
Sector 3: If you keep the truce up, you can actually skip the dialogue in the cutscene afterwards right after Vateilika kills Krotera. Aka, most of the scene.
Sector 4: Also, if you keep the truce up, no reboot needed, as you won't have thrown the points into Attack/Tasen/Assimilate.
Sector 9/X: You might look into grabbing Ansaksie here(and by extension, the Massacre in Sector X), but it's a long shot. If you do, the idea is to manipulate Ansaksie into spamming her Massacre on Iosa, as it's by far the fastest way to end the fight. She's unlocked by getting the supercharge in Deep Sector(and subsequently killing yourself to warp back to the Tasen base). The Massacre speeds up Tor dramatically(about 2.5 waves versus 6), but requires 0 kills up until that point, meaning you need to grab Ansaksie(which as mentioned, takes a good 30 seconds minus what she saves in the Iosa fight).