Basically two things were happening. For some reason apacite is not working no matter what I do. Also, some of the examples I sent did have the references file as .tex, not .bib files. I apologize for the second thing. This was stupid by me and probably caused by panic at my thesis not working.
I have now got the MWE to work with natbib but apacite does not work no matter what I do. With time running out with my thesis, I have actually thought it easier to just change from apacite to natbib. I've had to change all of my citation commands (e.g. \shortcite to \citep), and yes this was painful in a 250 page thesis








Another error I noticed was some references were corrupt in my thesis references file. I have managed to find all of these (about 10 in about 500). Also, some of the functions in the text automatically changed to what they were trying to print (e.g $/pm$ change to the actual +- sign). Both of these things were completely fine on my original computer so I'm not sure what went wrong. Again I have painfully now found all of these issues so back on track.
Regarding this last point, do you know of any good sources explaining how to safely transfer over latex documents? I had my whole thesis in one main directory (with many sub-directories), which was all copied over, but maybe I missed something in another file. For example, are there any settings MiKTeX or Texmaker uses to configure previous settings or configurations on a new computer (with new MiKTeX and Texmaker downloads), which I maybe forgot to copy over?
In summary, i) I made some mistakes in the MWE I sent you (apologies for this), ii) some of my thesis files seemed to be corrupt or missing or something but I have painfully fixed all these small errors, using natbib (instead of apacite) and some very very thorough error reading.
Thank you both once again for all the help.
Tim