It’s fine Mike. Here’s a copy of the original post i made in my thread which is in the plex pass part of the site:
Here is a set of scripts that you can use to automate mp4 creation of files.
I’d recommend running your files through FileBot first to rename them correctly before running them through this script. It can pull SRT files so everything ends up with proper names this way.
The only pre-requisite is to have python 2.7.9 installed. Python Release Python 2.7.9 | Python.org
(I’m running 64bit version for windows installed to C:\Python27)
This is a modified version of sickbeard_mp4_automator with modifications by me. I pulled out all the integration features to make setup much easier. I also modified it to produce higher quality MP4 files that will direct play better with Plex.
Download convert.zip from ftp://ayars.tv
username and password are both guest
Unzip to C: drive. You will end up with C:\Convert
There are two directories (can be changed) inside this folder that are used for the media
Process is where you put any files you want to convert
Done is where the files will end up after processing
You can run this multiple ways but the easiest is to use the Run.bat file.
If you edit this file you will notice it’s one line that reads: c:\python27\python manual.py -a -i c:\convert\process
If you install python to a different folder then change the python directory at the beginning of this line.
If you want to process files from a different location then c:\convert\process then just change this in the batch file.
If you want to change the final location of where the final files are stored then edit autoProcess.ini file and change the output_directory setting.
That’s pretty much it.
Put files in the process directory and run the batch file
What this will do:
It will process each and every file in the “process” directory.
It will remux files that are h.264 and will transcode files that aren’t h.264 video
It will pull out any english subtitles and create SRT files from them. If you want to pull out other languages then modify the subtitle-language setting in the ini file. Multiple languages are supported by commas
The completed file will not have subtitles (we pulled them out)
It will clear all tags in the mp4 file so Plex doesn’t pick up and use these tags instead of the proper meta-data
It will create an AAC track as the first track upto 256K in size.
It will remove all audio tracks not in english. If you want other languages included modify audio-language setting (ini file) and include any languages you want kept in the MP4 file. Multiple languages are supported by commas
When it transcodes it wil use an h.264 profile of high; a level of 4.0; crf setting of 20. These are basically the same as Handbrake High Profile settings with a bit more refinement for Plex use that allows it to direct play more often.
In all cases the final MP4 file has the MOOV ATOM at the beginning of the file (ie web optimized)
Advanced setting:
You can limit the total bitrate for the video. If for example you use a client that has an upper limit of 12000 KB you can set the option video-bitrate option to something like 11000 which gives you a bit of headroom for a couple of audio tracks.
There is more that can be done with this set of scripts but lets start off with these. 
Let me know what you guys think,
Carlo