Sorry I forgot all about this thread once it rolled off the first page. I was working with muffinmcfluffin on all the steps so I'm just going to reprint what I wrote to him. The goal of this was to get a MKV or a Blu-ray using free software. Any NLE would make this a lot easier but would cost a lot more money. The MKV works fine but we are still working on the Blu-ray. So you need to rip the main movie off the disc to a mkv or m2ts. So you should have a MKV or m2ts about 35 GB in size.
Open Handbrake. Click on Source and File and open the MKV/m2ts that you created. The profile on the left should be regular/normal. On the Output Setting pull down select MKV. Under Destination create the name/path of the new file. On the Picture tab under Size go to the anamorphic pull-down and select none. Set the width to 1920 and the Height to 800 (this will give you 2.40 aspect ratio). Under Cropping set the Top and Bottom to 140. All of this will give you a center 2.40 aspect ratio that matches the 35mm scenes.
In Handbrake select the Video tab. Leave the codec as h.264 and Framerate as same as source. Click on Avg Bitrate and enter 26000 (26000 kbps) which is roughly the same bitrate as the original Blu-ray. (If you are making a Blu-ray this will require a 50 GB disc. If you want to use a 25 GB disc set the bitrate to 15000). Check 2-Pass Encoding and Turbo first Pass. Use Constant framerate unlike in this picture.
Select the audio tab. The default audio source should be the Engligh DTS-HD MA soundtrack. On the drop down next to it select DTS-HD Passthrough
Click start. This will take a few hours. You should now have a 1920x800/ 2.39 MKV.
That is for the MKV. To convert that MKV to a Blu-ray, muffinmcfluffin and myself are still working the bugs out. I have a 25GB blu-ray that is cropped but for some reason the DTS-HD MA soundtrack is not working (mediainfo show it is there) so I need to track down where it is getting stripped. If anyone wants the instructions to convert it to a Blu-ray, let me know.
Also this will work for the Dark Knight but handbrake does not have a DolbyTrue passthrough. In that case you have to demux the Dolby True and remux it back using MKVmerge.