Hey Yar, guess i can try and help out here. Within each merge that needs multiple conflicts resolved, just click the arrow in the toolbar to hop down to the next highlighted error, then right click said text, and select which window you want to use script from (a b or c). I have found that not all of the conflicts in the guide are currently conflicting with the new versions of the mods. As long as you are fixing conflicts, then you should be good (as of a few weeks ago....) This vid does a much better job of explaining it. It is also on the script merger nexus page.
Also, thank you to everyone for all the work that was put into this guide. Can't wait till everything is updated so i can finally, probably, finish TW3.