Okay, I enabled the Query Diagnostics plugin. None of the queries is taking a long time, it’s just that there are 557 of them instead of the usual much fewer amount.
Most of the quereies are:
SELECT option_value FROM wp_options WHERE option_name = 'siteurl' LIMIT 1
or
SELECT option_value FROM wp_options WHERE option_name = 'home' LIMIT 1
So, everytime the script is referencing those values, it’s requerying MySQL instead of using a variable cache.
Again, I’ve already tried disabling all my plugins, using the default templates instead, and reinstalling all of the WordPress files, to no affect/change.