I would try taking note of the exact point where the encode fails.
Then go into the Sequence and see if there is a suspicious
media file at that point in the Timeline.
Then you can try to export only the segment where it continually fails
to determine if the problem is a specific file in your Timeline.
(use the Work Area Bar to define a partial export of your Timeline).
How to you know where the exact point is where it gets caught in the encode?
You watch the encode as it is running (queued in Media Encoder).
Adobe Media Encoder:
Edit > Preferences > Preview while encoding (checked)
You already know it crashes at around 41%...