You should be able to use Templater to do both. After you’ve located the folder into which you want to move the markdown file, you should also be able to follow suit and use javascript native functions to move the pdf file into the same path.
You’ll most likely need to figure out the full path, but there exists functions like the getAbsolutePath() (I think it’s called) which is somewhere in the Obsidian API :-), and other utility functions which can be used to find the full path.
However, the automation of such a task do require some knowledge of both scripting and file handling, and I would strongly suggest not to use any chat robot to generate such a script and running it blindly on your file system. I’d rather take my time and search for similar topics in this (and other) forum(s), and build it up piece by piece. After all, messing with thousands of files is something you’ll need to do with care.