FFMPEG/MP4Box converting M4V to MP4

[can]

So, I guess I should admit that this is an iTunes download, and yes there is no DRM on this file. And Yes, I have already demuxed and remuxed this file.

However, I wasn't able to include the subtitles and chapters in my remuxed MP4

So you understand what I am working with, I'll post the details of the 'file'

Video #1
ID                          : 1
Format                      : AVC
Format/Info                 : Advanced Video Codec
Format profile              : High@L4
Format settings, CABAC      : Yes
Format settings, ReFrames   : 4 frames
Codec ID                    : avc1
Codec ID/Info               : Advanced Video Coding
Duration                    : 1h 15mn
Bit rate                    : 5 152 Kbps
Width                       : 1 912 pixels
Height                      : 1 072 pixels
Display aspect ratio        : 16:9
Frame rate mode             : Constant
Frame rate                  : 23.976 fps
Color space                 : YUV
Chroma subsampling          : 4:2:0
Bit depth                   : 8 bits
Scan type                   : Progressive
Bits/(Pixel*Frame)          : 0.105
Stream size                 : 2.72 GiB (90%)
Title                       : Core Media Video
Language                    : English
Encoded date                : UTC 2015-11-11 09:06:29
Tagged date                 : UTC 2015-11-11 09:06:36
Color range                 : Limited
Color primaries             : BT.709
Transfer characteristics    : BT.709
Matrix coefficients         : BT.709


Video #2
ID                          : 5
Format                      : JPEG
Codec ID                    : jpeg
Duration                    : 1h 15mn
Bit rate mode               : Variable
Bit rate                    : 4 066 bps
Width                       : 640 pixels
Height                      : 357 pixels
Display aspect ratio        : 1.85:1
Frame rate mode             : Variable
Frame rate                  : 0.002 fps
Minimum frame rate          : 0.002 fps
Maximum frame rate          : 0.004 fps
Color space                 : YUV
Chroma subsampling          : 4:4:4
Bit depth                   : 8 bits
Scan type                   : Progressive
Compression mode            : Lossy
Bits/(Pixel*Frame)          : 8.898
Stream size                 : 1.94 MiB (0%)
Title                       : Core Media Video
Encoded date                : UTC 2015-11-11 09:06:29
Tagged date                 : UTC 2015-11-11 09:06:36


Audio #1
ID                          : 2
Format                      : AAC
Format/Info                 : Advanced Audio Codec
Format profile              : LC
Codec ID                    : 40
Duration                    : 1h 15mn
Source duration             : 1h 15mn
Bit rate mode               : Variable
Bit rate                    : 160 Kbps
Maximum bit rate            : 258 Kbps
Channel(s)                  : 2 channels
Channel positions           : Front: L R
Sampling rate               : 48.0 KHz
Compression mode            : Lossy
Stream size                 : 85.3 MiB (3%)
Source stream size          : 85.3 MiB (3%)
Title                       : Core Media Audio
Language                    : English
Encoded date                : UTC 2015-11-11 09:06:29
Tagged date                 : UTC 2015-11-11 09:06:36


Audio #2
ID                          : 6
Format                      : AC-3
Format/Info                 : Audio Coding 3
Mode extension              : CM (complete main)
Format settings, Endianness : Big
Codec ID                    : ac-3
Duration                    : 1h 15mn
Bit rate mode               : Constant
Bit rate                    : 384 Kbps
Channel(s)                  : 6 channels
Channel positions           : Front: L C R, Side: L R, LFE
Sampling rate               : 48.0 KHz
Bit depth                   : 16 bits
Compression mode            : Lossy
Stream size                 : 208 MiB (7%)
Title                       : Core Media Audio
Language                    : English
Encoded date                : UTC 2015-11-11 09:06:29
Tagged date                 : UTC 2015-11-11 09:06:36


Text
ID                          : 3-CC1
Format                      : EIA-608
Muxing mode                 : Final Cut
Codec ID                    : c608
Duration                    : 1h 13mn
Bit rate mode               : Constant
Stream size                 : 0.00 Byte (0%)
Title                       : Core Media Closed Caption
Language                    : English
Encoded date                : UTC 2015-11-11 09:06:29
Tagged date                 : UTC 2015-11-11 09:06:36


Menu
ID                          : 4
Codec ID                    : tx3g
Duration                    : 1h 15mn
Title                       : Core Media Text
Language                    : English
Encoded date                : UTC 2015-11-11 09:06:29
Tagged date                 : UTC 2015-11-11 09:06:36
Bit rate mode               : CBR
00:00:00.000                : 1
00:09:33.000                : 2
00:19:47.000                : 3
00:30:07.000                : 4
00:39:45.000                : 5
00:50:30.000                : 6
01:00:30.000                : 7
01:10:58.000                : 8

The Best thing for me to point out is, right now I only have the Video #1 and Audio #1 in an MP4 file. However I am waiting to keep/include (copy) Video #1, Audio #1, Text and Menu into a mp4 file.

Is anyone able to help me with a command with FFMPEG and or MP4Box?

[cooper]

I've got a ton of AVI files I'll be transcoding to Theora and mp4 soon. One thing I can already tell you is that you should be using avconv, which is basically the encoding/recoding bits from ffmpeg branched out into another project. What parameters are you currently using and how well do you like their result?