There has long been some kind of server maintenance that runs circa 1am PST. You will experience an inability to connect for a good 15-20 minutes around that time, and some slowness for a while after.
Which is probably the overflowing server logs backing up, JUST like what was killing us before I killed off the custom themes.
Given what trash the front-end code is, I'd not be surprised if the back end code is flooding the logs daily. Seriously, go into /var/logs and have a good hard look.
Though a LOT of software is now silently throwing hordes of errors as new versions of PHP
finally make insecure outdated methodologies and redundancies invalid, obsolete, or just flat out no longer supported. The upgrade to php 5.4 caused a lot of problems, and between 5.5, 5.6 and the "hey mysql_ functions go take a flying leap" release candidate for PHP 7 (skipping 6 entirely) things are about to get very interesting... since 90% of existing PHP software won't run under 7.
Sometimes it's just simple stuff too... PHP 3 used to return null and not log an error if you called a variable without checking isset first - along comes PHP 4 and all that was invalid and threw errors. PHP 5 removed a lot of redundancies logging "warnings" and in later versions "errors" on simple stuff.
Every time you upgrade PHP now you have to go through and make sure any older existing software isn't tossing it's cookies all over the place. ADMITTEDLY it's simplifying the language and encouraging more secure practices, but at the same time it can be a real pain in the backside.
We're probably gonna see the nonsense practice of running PHP 5 alongside PHP 7 coming into bloom pretty soon - just like people were doing with PHP 4 and 5.
