Just made this for personal use and thought I'd share. It's a simple mux of Doki's subtitles/chapters with Yousei-raws' encode. Don't like the dub enough to properly sync and make signs/songs for 24 episodes.
The BDs are terrible for the first two seasons (Funimation's DVDs are downscaled from this). The R2J DVD encodes mentioned below are recommended:
[Doki's DVD release](https://nyaa.si/view/925317) for the first season.
SumiSora & Ktxp's DVD encode muxed with subtitles is probably the best option for the second season. As far as I know, the only options for subtitles are [SS-Eclipse](https://nyaa.si/view/158744) and the [official ones](https://kitsunekko.net/dirlist.php?dir=subtitles%2FShakugan+no+Shana+II%2F) (Exiled-Destiny in the link).