You should not be rendering MP4's a digital intermediate. You should use a visually lossless frame-based format. For your own good do some studying about video formats and production formats. Editing is almost always easier in Premiere Pro, especially if there is audio and sound effects in the project. If all you are doing is cutting together shots it is possible to select all of the comps in the Project Panel in order and then use File>Create Composition from Selected, then choose sequence layers. This will get you close to a final picture edit, but long comps with lots of layers and effects can be a chancy proposition. If you go directly to the Adobe Media Encoder and the render fales, you'll have a devil of a time avoiding trying the entire render all over again. For long projects, basically, anything that is going to take what you consider a long time to render, It is always a good idea to render an image sequence. If an image sequence render fails at frame 1700, and it took you 3 hours to get there, and you only have a hundred frames to go you can set the work area to frame 1701, figure out what caused the failure, then render the last 100 frames and be done. If you were rendering video using almost any format and certainly if you were rendering an h.264 (MPEG), you would have to start over at the first frame.
Most newbies that hear these suggestions balk at rendering twice, creating production masters, the storage space required for lossless formats and the perceived extra work of rendering shots in AE then editing them in an NLE like Premiere Pro. If the one step comp to final video render was the most efficient and economical then all of the top end production companies would be doing it that way. In reality, none of them do. Effects shots and animations are rendered to a suitable production format, the editing is done in an NLE, the sound is almost always fine-tuned in a sound app like Audition, and then the final color correction is made and the production master is rendered. The final lossless production master is used to render the compressed versions for distribution. In the long run, it takes less time and you end up with a much better project because you have more time to make the kind of decisions that can improve the story.
I see that your master comp is almost 3 minutes long and that there are 20 video tracks and one audio track. There is a comp with two layers that is about one second long that contains a fox with no background. That appears to be nested in layer 13 with is about 30 seconds long. I'm a little confused about what is going on there. I'm assuming that if layer 13 was opened up that we would see several shots. If that is the case then I would probably render layer 13 and edit it into the sequence in an NLE. I have no idea what is going on in the rest of the comp so I would need to see a flow chart and probably a storyboard to decide on the most efficient workflow.
Generally, if you have a sentence of dialogue or narration or a phrase of music that needs two or three shots it can be efficient to make the sentence or phrase a single comp. If you have a couple of paragraphs or 8 bars of a song to cover, it's a good idea to pre-edit that in your mind and figure out where the cut points will be and break it up into separate comps. I would guess that your Master comp could easily be broken up into 4 or 5 shorter comps. Depending on the audio track and the shots, you may be better off doing all of the compositing in each of the 18 or so nested comps you have created, rendering each separately, then editing the piece in an NLE so you can fine-tune the performances.
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