[colours]

I'm just going to give some generic advice here.

Firstly, this is obviously a rule 6 violation, though I guess this stopped mattering when neuron2 became Guest.

Secondly, if you're looking for help with encoding for fansubs, ask other fansubbers. I hear this is a problem that they have researched reasonably well and have existing solutions for.

Thirdly, anime series licensed from TV Tokyo on Crunchyroll and Funimation tend to have IVTC-related issues, and these issues are usually inconsistent between episodes. A majority of Funimation's streams are fine, but this particular series you're using as an example is not.

Fourthly, you should ensure that the clips align as well as possible, both spatially and temporally. The aforementioned IVTC issues essentially guarantee that temporal alignment will require duplicating and deleting frames at random places (use a script, obviously; doing this manually is insane and a complete waste of time). As for spatial alignment, cropping the subtitle-free source by two pixels on the left and right sides is obviously not the right thing to do, as a frame comparison would tell you; all you have to do is to resize to 720p and you're done.