Connectivity couldn't have caused the copy failure.
The only error that might be related to that is this one (and it could possibly have been caused by the failure to copy the files):
[2017-01-12 12:53:55] (ERROR @ /home/../public_html/../core/xpdo/transport/xpdoobjectvehicle.class.php : 228) Could not resolve vehicle for object of class modContext; criteria: Array
(
[key] => web
)
At any rate, if the files can't be copied, the upgrade isn't going to work. Since permissions and disk space are OK, my money would be on file ownership, though that's not an area of expertise for me.
All that said, I would be tempted to just upgrade the old fashioned way as AndyTough suggests, using this method:
http://bobsguides.com/modx-upgrade-faq.html. Be sure to manually delete all files in the core/cache directory before logging in.
[Update] This just occurred to me and it seems pretty unlikely, but if the file extraction timed out, maybe some of the files to be copied didn't get extracted, and thus didn't exist, and that's why the copy actions failed. Again, probably the best solution is to just do an old-fashioned upgrade.
[ed. note: BobRay last edited this post 7 years, 2 months ago.]