What you need:
MKVToolnix - Install where you want it.
MKVextractGUI/MKVE Wizard - Use the GUI or the Wizard, but only ONE of them. Drag the appropriate files into your MKVtoolNix Directory
MeGUI - Install where you want it.
Nero AAC Codec - Drop the files for your system into the same directory as MeGUI.exe
Avisynth - Install where you want it.
VSfilter textsub - Drop the files into the "plugins" folder of Avisynth's Directory.
Now pick the anime you want, The instructions will be based on doing this with a full series.
1) Open up MKVExtractGUI (Or MKVE Wizard if you're using that UI instead, they both function about the same).
2) Drag the first episode of the anime you want and drop it onto the "Input" field.
2a) Pick your output directory, default is it'll drop the extracted files into the directory with your anime, that's what I did. I you want to change it just click the "other" bullet and tell it where to put them.
3) Check the boxes for extraction of the Audio, and Subtitle streams you want to hard code into your final result. You must also extract all Fonts these appear as 'Attachment ID's. DO NOT EXTRACT VIDEO this takes a LONG time and you won't need it.
4) When everything you want extracted is checked, click the 'Extract" button. The program will appear to not do anything, but you will see a bar appear at the bottom... it never moved for me, but that was my signal it was at least working, also the files will begin appearing in your output directory. (It took my system about 20-40 seconds to extract everything, results may vary greatly, I've got a pretty high level system.)
4a) Rinse and repeat from step 2) for all episodes you want to re-encode. You don't have to continuously extract the fonts as long as they remain the same ones for the entire anime, the one I did (
Macross Frontier [Thora]) had about 4-5 fonts used in every episode with an extra 10 or so that only appeared in 1 or 2 episodes each, so make sure you pay attention to the fonts and get them all.
4b) We're done with MKVtoolnix, you can close it. You may want to check the audio files to make sure they play.
5) Now it's time to Re-encode the Audio. Open MeGUI (if it needs to update, do so, then import all the stuff it asks about importing) and drag you first episode .ac3 file into the Input Field of the Audio section (lower half of the window).
6)Change Encoder settings to Nero AAC: pick the quality you want, I personally did MultiChannel HQ 256.
7)Press the Enqueue Button
7a) Rinse and repeat from step 5) for all .ac3 files you want to process.
Switch over to the Queue tab and Click Start. (you may want to edit some settings first from the options-> Settings menu, like setting default priority to 'above normal').
9)Time to Wait. This took my system about 30 seconds per file, results may vary. About 15-20 minutes for my entire batch (25 episodes).
9a) When it's done check the audio again, and you can delete the .ac3 files unless you want to keep them incase something went wrong you didn't notice.
Time to make your AviSynth Scripts. For this portion I'm going to use the names/directories/code of the files I made. Follow the format with your own file information.
Your .asv file name will be the name of your final ouput video... sort of.
10)First Episode .asv file:
Macross F - 01 - Close Encounter1.asv - I added the '1' to the end of the file because your 'video only' .mp4 will take this name, adn be deleted later.
DirectShowSource("D:\Anime\Macross Frontier\Macross F - 02 - Hard Chase [THORA].mkv", fps=23.976, audio=false)
TextSub("D:\Anime\Macross Frontier\Macross F - 02 - Hard Chase [THORA]_Track3.ass")
Note that the DirectShowSource file is the original .mkv that the sub group made, TextSub is pointing to the Subtitles you extracted with MKVExtractGUI.
11) Make all your .asv files now, it'll speed up making the job queue's in MeGUI. Follow the format above and have a different .asv file for each episode. Place these files in the directory you want your final result .mp4 to be in.
12)Drag and drop the first episode .asv file into the AviSynth Script field of MeGUI (top half of the window this time).
12a)Note the Video Output field auto fills in, this is your 'video only' and will be deleted later, unless it's the exact name you want your end result file to be, don't change it.
13) Click the auto Encode button in the button right to open a new window.
14) The 'Name of Output' field is the directory and name of your final result. It will have your .asv name with a -muxed added to the end. Change it to what you want your final result to be.
15) Make sure the "Add additional content) box IS CHECKED, then click the Queue button for yet another new window. If you don't check that box you'll get no new window and end up with a video with no sound.
16) On the New window Drag and drop the _Track2.mp4 you extracted from the original .mkv into the 'Audio 1' input field, select the language, and click GO.
17) All the extra windows should close Leaving you looking at teh main MeGUI window again, CLick the queue tab and you'll see 2 jobs for that episode first video, then mux.
18) Rinse and repeat from step 12) until you have jobs for all the episodes you are doing.
18a) ONe thing That happened to me, When I started, it did one episode then stopped, so I checked the option to "autostart queue" AFTER I had everything Queued, and it went from job to job with no issues for me after that.
19) Click the Queue tab, and click Start. Find a good time when you don't plan on using your computer for a VERY long time. My system was doing a single episode in about 1 hour. The good thing is, you can abort a job, right click it and change the status back to 'waiting' Then use your pc, shut it down, watch anime, whatever. MeGUI saves your jobs even when it's turned off so you don't have to redo any of the creation process, just open it back up and start them up again.
20) Enjoy .mp4's with hardcoded stylized subs exactly as they were in their .mkv versions.
