Just integrate all filtering into one command:
ffmpeg -i input.mp4 \
-filter_complex "[0:v]crop=in_w/2:in_h:0:0 [top]; \
[0:v]crop=in_w/2:in_h:in_w/2:0[bottom]; \
[top][bottom]vstack[outv]" \
-map "[outv]" -map 0:a -c:a copy output_3dv.mp4
Edit: this command below scales and pads the output to 2000x2000
ffmpeg -i input.mp4 \
-filter_complex "[0:v]crop=in_w/2:in_h:0:0 [top]; \
[0:v]crop=in_w/2:in_h:in_w/2:0[bottom]; \
[top][bottom]vstack,\
scale=iw*min(2000/iw\,2000/ih):ih*min(2000/iw\,2000/ih), \
pad=2000:2000:(ow-iw)/2:(oh-ih)/2[outv]" \
-map "[outv]" -map 0:a -c:a copy output_3dv.mp4