Funscripts and Files in nested folders

Before moving to Stash I had all my funscripts in one folder and then all my videos seperated in a different folder that has nested folders to organize them. Is there a way to make stash recognize the funscripts for each video without the files needing to be in the same folder? Or alternatively is there an easy way to move all my funscripts to where the corresponding video is?

No. You would need to modify the source code to change the logic and build a new release.

You could write a script to do that, but apart from that I don’t know of any tool that can do that.

File names need to match scripts for stash to detect them so you need video.mp4 and video.funscript for stash to detect it.
I am building up a database of what script goes to what file in timestamp.trade.
The data is crowd sourced and uses the hash of the funscript file to find matches.
To submit data you to have matched the script to the scene and to have run the “Index Funscript” and run the “Submit Scenes with a funscript” task.
To turn on the feature enable “Match funscripts” in the settings page and run the " Index Funscript" task then one of the reprocess tasks “Re-process Scene” or “Process All”.