Hello,
it's well known, that in all these cases you describe I'm not a friend of a detailed troubleshooting. To be able to be independent in all this things It is one of the reasons why I prefer an external FTP program. The difficulties with which you have to fight encourage me in this opinion, not least because we always search for experts, we don't charge a "jack of all trades".
To manage several websites or to upload my files and sometimes for the opposite way, for a necessary download from my server or to use a "a site-wide synch", I'm using FileZilla. It simply looks easier for me to keep track of all operations precisely and generate or reflect easily the desired tree structure.
Above all, FileZilla has a feature (translation from my German FileZilla) called "compare file list". Here it's possible to use file size or modification time as a criterion. There is also the possibility to "hide identical files", so that only these files which you want to redact remain visible.
And even if it means you have to install a new program, I am convinced that there is an advantage. Here is the link to get it and where you can read informations about how it works:
Mac: Mac OS X (Use: Show additional download options)
http://filezilla-project.org/download.php and see translation for japanese addition https://filezilla-project.org/translations.php
Of course, you also need all the access data to reach your server and for MIME issues, you should contact your web host/provider.
Good luck!
Hans-Günter
P.S.
I'll try to get a translation into Japanese language.