Descobri que os vídeos são 640X480 e os rodados são 480X640. Aqui estão quatro cenários. Espero que ajude alguém no futuro. :)
{filenumber} = {angle}
1 = 90 2 = 0 3 = 0 4 = 0
ffmpeg.exe -i "1.avi" -vf "[in] scale=0:480 , pad=width=640+640:height=480:x=(640-480)/2:y=0:color=red [left];movie=2.avi, scale=640:480, pad=width=640:height=480:x=0:y=0:color=red [right]; [left][right] overlay=640:0 [out]" -b:v 768k "Output1.mp4"
ffmpeg.exe -i "3.avi" -vf "[in] scale=0:0 , pad=width=640+640:height=480:x=0:y=0:color=red [left];movie=4.avi, scale=0:0, pad=width=640:height=480:x=0:y=0:color=red [right]; [left][right] overlay=640:0 [out]" -b:v 768k "Output2.mp4"
ffmpeg.exe -i "Output1.mp4" -vf "pad=iw:2*ih [top]; movie=Output2.mp4 [bottom]; [top][bottom] overlay=0:main_h/2" "Output_Stacked.mp4"
Pause
2 = 0 1 = 90 3 = 0 4 = 0
ffmpeg.exe -i "2.avi" -vf "[in] scale=0:0 , pad=width=640+640:height=480:x=0:y=0:color=red [left];movie=1.avi, scale=0:480 , pad=width=640:height=480:x=(640-480)/2:y=0:color=red [right]; [left][right] overlay=640:0 [out]" -b:v 768k "Output1.mp4"
ffmpeg.exe -i "3.avi" -vf "[in] scale=iw:ih, pad=2*iw:ih [left];movie=4.avi, scale=iw:ih [right]; [left][right] overlay=main_w/2:0 [out]" -b:v 768k "Output2.mp4"
ffmpeg.exe -i "Output1.mp4" -vf "pad=iw:2*ih [top]; movie=Output2.mp4 [bottom]; [top][bottom] overlay=0:main_h/2" "Output_Stacked.mp4"
Pause
90 90 0 0
ffmpeg.exe -i "2.avi" -vf "[in] scale=0:480 , pad=width=640+640:height=480:x=(640-480)/2:y=0:color=red [left];movie=1.avi, scale=0:480 , pad=width=640:height=480:x=(640-480)/2:y=0:color=red [right]; [left][right] overlay=640:0 [out]" -b:v 768k "Output1.mp4"
ffmpeg.exe -i "3.avi" -vf "[in] scale=iw:ih, pad=2*iw:ih [left];movie=4.avi, scale=iw:ih [right]; [left][right] overlay=main_w/2:0 [out]" -b:v 768k "Output2.mp4"
ffmpeg.exe -i "Output1.mp4" -vf "pad=iw:2*ih [top]; movie=Output2.mp4 [bottom]; [top][bottom] overlay=0:main_h/2" "Output_Stacked.mp4"
Pause
<90> 90 90 90
ffmpeg.exe -i "1.avi" -vf "[in] scale=0:0 , pad=width=480+480:height=640:x=0:y=0:color=red [left];movie=2.avi, scale=0:0 , pad=width=480:height=640:x=0:y=0:color=red [right]; [left][right] overlay=480:0 [out]" -b:v 768k "Output1.mp4"
ffmpeg.exe -i "3.avi" -vf "[in] scale=0:0 , pad=width=480+480:height=640:x=0:y=0:color=red [left];movie=4.avi, scale=0:0 , pad=width=480:height=640:x=0:y=0:color=red [right]; [left][right] overlay=480:0 [out]" -b:v 768k "Output2.mp4"
ffmpeg.exe -i "Output1.mp4" -vf "pad=iw:2*ih [top]; movie=Output2.mp4 [bottom]; [top][bottom] overlay=0:main_h/2" "Output_Stacked.mp4"
Pause
90 90 0 90
ffmpeg.exe -i "1.avi" -vf "[in] scale=0:0 , pad=width=480+480:height=640:x=0:y=0:color=red [left];movie=2.avi, scale=0:0 , pad=width=480:height=640:x=0:y=0:color=red [right]; [left][right] overlay=480:0 [out]" -b:v 768k "Output1.mp4"
ffmpeg.exe -i "3.avi" -vf "[in] scale=480:0 , pad=width=480+480:height=640:x=0:y=(640-480)/2:color=red [left];movie=4.avi, scale=0:0 , pad=width=480:height=640:x=0:y=0:color=red [right]; [left][right] overlay=480:0 [out]" -b:v 768k "Output2.mp4"
ffmpeg.exe -i "Output1.mp4" -vf "pad=iw:2*ih [top]; movie=Output2.mp4 [bottom]; [top][bottom] overlay=0:main_h/2" "Output_Stacked.mp4"
Pause