...getting all kinds of htaccess issues and 404/401s on css and navigation is all off.
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MODX is a PHP script, nothing more, nothing less. What web server is being used is irrelevant to MODX. The .htaccess or other web server rewrite rules do nothing more than load the MODX index.php file if the web server can't find a file or a directory that has been requested.
The friendly urls part of the default revo .htaccess file resulted in 401 and 404 errors in Apache 2.4 for css and images. When I switched back to apache 2 it was all good. cPanel tech support spent an hour looking at the issue and concluded the above.
I just put a site on SkyToaster, running Apache 2.4.12 and MySQL 5.4.39, and it works fine.