Workflow:

1) Scan Tailor Universal - process images

yay -S scantailor-universal-git

Scale fix:
cp /usr/share/applications/scantailor-universal.desktop ~/.local/share/applications/
nano ~/.local/share/applications/scantailor-universal.desktop
Add: env QT_SCREEN_SCALE_FACTORS=2.0
update-desktop-database ~/.local/share/applications
Reboot

Dark mode:
adwaita-qt5-git

2) sep.sh - encode DjVu

#!/bin/bash

# configuration
DPI=600
OUT_NAME="final.djvu"
TEMP_DIR="tmp"

mkdir -p "$TEMP_DIR"

# loop through layer files
for text_layer in *.tif; do
    # skip .sep.tif files
    [[ "$text_layer" == *.sep.tif ]] && continue
   
    base=$(basename "$text_layer" .tif)
    illus_layer="${base}.sep.tif"
   
    echo "Processing Page: $base"

    # foreground
    # create bitonal mask chunk (Sjbz)
    cjb2 -dpi $DPI "$text_layer" "$TEMP_DIR/$base.fg.djvu"

    # backgroud
    if [ -f "$illus_layer" ]; then
        # convert to PPM
        magick "$illus_layer" "$TEMP_DIR/$base.bg.ppm"
       
        # create temporary photo DjVu
        c44 -dpi $DPI "$TEMP_DIR/$base.bg.ppm" "$TEMP_DIR/$base.bg.djvu"
       
        # extract IW44 chunk
        djvuextract "$TEMP_DIR/$base.bg.djvu" BG44="$TEMP_DIR/$base.bg.chunk"

        # assemble masked page
        djvumake "$TEMP_DIR/$base.combined.djvu" \
            "INFO=,,$DPI" \
            Sjbz="$TEMP_DIR/$base.fg.djvu" \
            BG44="$TEMP_DIR/$base.bg.chunk"
    else
        # no illustrations - just use the text layer
        cp "$TEMP_DIR/$base.fg.djvu" "$TEMP_DIR/$base.combined.djvu"
    fi
done

# bind all pages
echo "Bundling into $OUT_NAME..."
djvm -c "$OUT_NAME" "$TEMP_DIR"/*.combined.djvu

# clean up
rm -rf "$TEMP_DIR"
echo "Done."

3) FineReader 15 - OCR

Wine

4) FR crutch - insert OCR layer

Wine

5) bookmark-djvu - insert contents

yay -S bookmark-djvu

6) Document Express Editor 6 - insert cover

Wine