MKV/H.264: AR Change + Audio & Subs Mux

[Tormanoid]

Hey guys. Newbie here.

So.. I've got some MKV videos, that mostly look like these (through MediaInfo):

General
Complete name                            : X:\XXX\123.mp4
Format                                   : MPEG-4
Format profile                           : Base Media
Codec ID                                 : isom
File size                                : 1.10 GiB
Duration                                 : 2h 45mn
Overall bit rate mode                    : Variable
Overall bit rate                         : 952 Kbps
Encoded date                             : UTC 2013-03-26 07:00:52
Tagged date                              : UTC 2013-03-26 07:00:52

Video
ID                                       : 1
Format                                   : AVC
Format/Info                              : Advanced Video Codec
Format profile                           : High@L4.0
Format settings, CABAC                   : Yes
Format settings, ReFrames                : 8 frames
Codec ID                                 : avc1
Codec ID/Info                            : Advanced Video Coding
Duration                                 : 2h 45mn
Bit rate                                 : 852 Kbps
Maximum bit rate                         : 6 085 Kbps
Width                                    : 1 280 pixels
Height                                   : 536 pixels
Display aspect ratio                     : 2.40:1
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)                       : 0.052
Stream size                              : 1 008 MiB (89%)
Title                                    : 123.mkv.264#trackID=1:fps=23.976@GPAC0.5.1-DEV-rev4283
Writing library                          : x264 core 129 r2245 bc13772
Encoding settings                        : cabac=1 / ref=8 / deblock=1:-1:-1 / analyse=0x3:0x133 / me=umh / subme=9 / psy=1 / psy_rd=1.00:0.15 / mixed_ref=1 / me_range=16 / chroma_me=1 / trellis=2 / 8x8dct=1 / cqm=0 / deadzone=21,11 / fast_pskip=1 / chroma_qp_offset=-3 / threads=12 / lookahead_threads=2 / sliced_threads=0 / nr=0 / decimate=1 / interlaced=0 / bluray_compat=0 / constrained_intra=0 / bframes=3 / b_pyramid=2 / b_adapt=2 / b_bias=0 / direct=3 / weightb=1 / open_gop=0 / weightp=2 / keyint=240 / keyint_min=23 / scenecut=40 / intra_refresh=0 / rc_lookahead=60 / rc=2pass / mbtree=1 / bitrate=852 / ratetol=1.0 / qcomp=0.60 / qpmin=0 / qpmax=69 / qpstep=4 / cplxblur=20.0 / qblur=0.5 / ip_ratio=1.40 / aq=1:1.00
Encoded date                             : UTC 2013-03-26 07:00:52
Tagged date                              : UTC 2013-03-26 07:02:35

Audio
ID                                       : 2
Format                                   : AAC
Format/Info                              : Advanced Audio Codec
Format profile                           : LC
Codec ID                                 : 40
Duration                                 : 2h 45mn
Bit rate mode                            : Variable
Bit rate                                 : 96.0 Kbps
Maximum bit rate                         : 136 Kbps
Channel(s)                               : 2 channels
Channel positions                        : Front: L R
Sampling rate                            : 48.0 KHz
Compression mode                         : Lossy
Stream size                              : 114 MiB (10%)
Language                                 : English
Encoded date                             : UTC 2013-03-26 04:25:24
Tagged date                              : UTC 2013-03-26 07:02:35

Three issues with these are:

- They already come with embedded SRT subtitles in a foreign language.
- The 2:40 Aspect Ratio is a bit too wide for my taste, I'd like to change it to 2:25.
- The audio volume level changes drastically everytime. So I extract the audio and apply compression to attenuate loud transients, save to lossless audio file, and watch the clip on MPC with my custom-made file as the selected audio source (on the fly, no mux needed).

Normally I watch these in my PC, but since I want to now watch them in a LCD TV, I've to correct some things:

1. Remove the embedded SRT subs, and replace it with my own.
2. Change AR without re-encoding.
3. Replace the AAC file, with my own custom version of it (now using AAC instead of lossless).

Preferably in one go.

I already have the SRT and the audio work is done. I just need to put everything together.
I already have a few tools to work with:
- mkvmerge GUI v6.1.0 ('Old Devil')
- tsMuxeR GUI 1.10.6
- Yamb 1.6.0
- AVI-Mux_GUI-1.17.8.3

But I don't know how to used them properly (what's the whole ts and m2ts??).

However, maybe you can suggest other software (or different/proper version of the one I already have). I've seen you guys work with command line programs, but I'm clueless about how to use those. GUIs are easier for me, although I could learn to use commands (in case these work better, or if there's no other way).

I hope you guys can help me.

[Baldrick]

YOu can do most with mkvmergegui. Replace subtitles, change display aspect ratio(BUT this will make the video look stretched and the player must support the mkv aspect ratio). and replace the audio.