The following command line uses ffmpeg to change an avi file to an mp4 file, while adding a stereo AAC audio track in stream one for Roku compatibility.
ffmpeg -i input.avi -map 0:v -c:v copy -map 0:a:0 -ac 2 -c:a libfdk_aac
-map 0:a -c:a:1 copy output.mp4
In retrospect, I wonder if the first -map 0:a:0 should be just -map 0:a.