Reason for config errors on the server for all sites:
There's a number of differences between the two servers starting with the operating system but most importantly it appears the source server uses mod_mpm_event whereas the destination uses mod_mpm_prefork. Usually we try to match this since it makes a difference with the errors you saw, it must have been missed. I can go ahead and match this before we do any of the resyncs as that may avoid the issues you were seeing on the Joomla sites.