Embedded Data not appearing in exported files

You would ONLY put the embedded data fields before the block. Putting them after would overwrite the values set by JavaScript.
The JS library you linked to hasn't worked for a few years, so I'm surprised it ever worked at all in your survey. I had a client that used to rely on it, and I had to write a replacement when it stopped working for them.
Based on what you've stated, if you added your matrix questions to the same block as your Stroop that probably caused the problem. They should be in a separate block.

TomG I noticed it was outdated, but I was able to collect data when I tried to use it so I assumed it was somehow still working. The matrix questions are in a separate block than the Stroop ones.
The embedded data could be anywhere before the block it is collecting data from OR it has to be directly before? Let's say the placement was in the incorrect spot when responses were collected. If it wasn't placed after the block and got rid of the values, can I still somehow access that data? Is there a way to retroactively collect that stuff?
Thank you for the reply!

The embedded data can be anywhere before the block as long as it is executed. The safest thing to do is put it at the very top of the survey flow. That way you don't run the risk of it being in a branch that isn't executed.
There isn't a way to record it retroactively. If it isn't in the survey flow, it acts as a temporary variable that is only available during the survey session.

TomG okay thank you so much for your help!