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The thing is you cant actually stop someone for stealing works from a PDF file. All safeguards save full file encryption is possible to overcome easily at current time. Simply, this is why copyright exists in first place.
See the problem is if you want to show somebody something in a PDF reader, then that reader needs to be able to open said resource. Now ...
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A partial answer
Some Bitstream fonts have the wanted pi. It seems to be just in Bitstream's implementation of the typeface, it isn't the same in versions made by others.
One example: Iowan Old Style Italic
Here's a few letters of it:
As you see the rest of the letters aren't the same, only the pi symbol (hex 0390) is the wanted one. There's only a few ...
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Don't think this is possible. (Apart from the method you mentioned that is locking both text and images).
But in this case you can draw these diagrams as vectors, which should solve this issue. If text of diagrams should remain non-copiable you would need to outline it. (But with many diagrams that might be too time consuming...)
Also about your other ...
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File > Scripts > Load files into Stack..
Select the files or a folder containing the files and sit back and wait...
Photoshop will open each PDF, copy it, and combine them all into a single document, one layer per file.
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