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I think you should probably go back to step one. You seem to have learned things either wrong or a long time ago (latter looks more likely). Things have changed in the meantime, there are new programs and better ways to do the same things or avoid issues entirely. Specifically, for subs... well, for starters you're supposed to be buying your footage, but in the assumption that you're, e.g., a subscriber to crunchyroll and using a show that's on there, it'd be a nice thing to keep in mind that most shows around are actually softsubbed, so you can just hide the subs from your footage and call it a day (crunchyroll videos are encoded directly from high bitrate masters and doesn't even add logos on the video, so it's not like you'd be dealing with poor 2k3 hardsubbed tvrips).
Read ErMaC & AbsoluteDestiny's Friendly AMV Guides Lovingly Overhauled Largely by Zarxrax
, as that's the closest to being an up-to-date guide-to-all-things for amvers. It is outdated itself too, but not as much as older things (I see amvapp3beta in the list, and that IS old, a few years older than amvapp 3.1, I believe).
Mostly you'd want to be using latest vdub
(either 1.9.11 stable or 1.10.3 experimental is fine), latest avisynth
(currently 2.6 alpha 4, which is what I suggest by now, though 2.5.8 is fine if you really really want to use a stable), and updated plugins (mostly ffvideosource
from ffms2-2.18-rc1.7z as of this post, as well as lwlibavvideosource
from L-SMASH-Works, which is at r593 right now, for 8bit video; other plugins aren't so much of a necessity nowadays with interlaced footage being somewhat rare as far as home video releases go, and the ones included in the plugins pack of the amvapp are fine for the job, in case); also do give a try to the latest zarxgui
as well. All the theory and most other things from the avtech are still fine.