Hi @Generous_photoec17 ,
Hope you are doing well, and thanks for the detailed write-up and the related threads.
This almost certainly comes down to how the 3rd party tool built the text layer during the merge, rather than anything wrong with Acrobat Reader itself. A PDF has two separate layers: the visible page content and an invisible text layer on top of it, used for selecting, searching, and copying text. When a PDF is produced by certain scanning, OCR, or third-party merge tools, the invisible text layer can end up with incorrect position data, so it marks a word as being in one spot on the page when it's actually rendered elsewhere. The page looks completely normal, but clicking to select grabs whatever the misplaced text layer thinks is there, rather than what you're pointing at. Browsers sometimes render this more forgivingly, which is likely why the file looked fine there.
Since you're on the free Reader, a couple of things are worth knowing:
Reader doesn't include a Combine Files tool or a Recognize Text/OCR tool; both are features of Acrobat Pro or Standard. So rebuilding the broken text layer isn't something Reader itself can do, and testing whether an Acrobat-native merge behaves differently isn't possible without a paid plan or trial.
What you can try within the Reader's tool-set:
Adobe offers free, browser-based tools at Acrobat online (no Reader installation needed), including a free Merge PDF tool, with one free use of the premium online tools every 30 days: https://adobe.ly/46685ut. Merging your original source files there instead of through a 3rd-party tool may produce a cleaner text layer, since Adobe's merge tool handles the underlying PDF structure differently than third-party tools do.
For more information on Acrobat's free online tools, check the help page here: https://adobe.ly/45RIOEt
Let us know how it goes.
Regards
Amal