The following recipe works for mux2: 

dd if=mux2.ts bs=1024 skip=488281 | vlc - --program 2000 --demux=ts --intf dummy --play-and-exit --noaudio --novideo --sout '#std{access=file,mux=ts,dst=foobar_first.ts}'
vlc mux2.ts --program 2000 --demux=ts --intf dummy --play-and-exit --sout-file-append --noaudio --novideo --sout '#std{access=file,mux=ts,dst=foobar_first.ts}'
dd if=mux2.ts bs=1024 count=488281 | vlc - --program 2000 --demux=ts --intf dummy --play-and-exit --sout-file-append --noaudio --novideo --sout '#std{access=file,mux=ts,dst=foobar_first.ts}'
HandBrakeCLI -i foobar_first.ts -r 24 -e x264 -E faac --crop 0:0:0:0 --height 240 --vb 400 --optimize -o foobar.mp4

Note that it uses vlc as a demuxer and HandBrake as a transcoder. The bitrate (-r 24) video codec (-e x264) and audio codec (-E faac) are all necessary for successful streaming in Wowza. The test was with vlc 1.1.2 and HandBrakeCLI version svn3510 on Ubuntu Linux.