This is makeMKV screen shot for disk 1. Disk 2 is similar. So your saying the 3.9GB file is all I need. I watched a minute or two of the smaller files (the 1.1GB and the 857MB) and they contained concert video too - but maybe those concerts are contained within the 3.9GB file. I suppose I need to watch more of the file to know.
Here's what I do when I'm ripping disks:
1. Open with MakeMKV and wait for it to finish processing the title sets.
2. Open the disc with VLC.
3. Navigate the disk in VLC to play the main movie.
4. When the main movie is playing, go to the Playback menu and go to Title to see which title is selected. That title number is the main title. In your case, it's almost certainly the 3.9 GB title.
5. Continue navigating via VLC to make sure I do or do not want the rest of the disk. This includes going to the special features menus and seeing if I want any of that stuff, etc.
6. If there are multiple audio options, I generally select them manually in VLC from the Audio menu to make sure I can hear the director's commentary, etc, as well as the main movie audio. This might include surround tracks, stereo tracks, and perhaps even foreign language tracks.
7. Using the information obtained above, I then select the title or titles I want to save and the audio track or tracks I want. I usually select the main subtitle track too, because it's almost zero storage size and might be useful at some point.
In the case of the Pulse DVD, I'm now remembering that disc 2 has LOTS of extra footage. It's primarily the graphics that they are showing on the projection screen in the concert hall during the concert. These extras are the graphics and animation "pure direct", in case you want to see them isolated from the concert footage. Like Roderick said, you'll need to go through them one by one and see if you want them. They are NOT part of the main concert though, so that might make it easier for you.
Good luck!
Brian.