Indeed, filter order plays a major importance in how the actual video ends up. You're always welcome to attach short sample clips from your source (max 7.9MB file size), as well as attach the VCF files (save processing settings). I can take a look at what you have, and see if there's anything I'd change, be it filter order or even the filters themselves.
I'd say lossless HuffYUV compression would be fine for you.
