Morning Slowdown on Website

I’ve got a tricky one here…

I use Hostmonster for my WordPress site. Every day around 2:00am, the site starts going slow, and speeds up in the late morning. I uses supercache, and it generates pages in .6-.7 seconds at the fast times, and 6-10 seconds with some 15+ seconds times during the slow period. My long mySQL query logs follow this same pattern.

I’m convinced it is a server side issue, since the effect is seen on other installs (i.e. limesurvey, moodle, phplist) and on my cPanel, but the host is focusing on my long queries. They say that the long queries could affect the other installs.

My user load patterns don’t match the site slowdown, plus I watch my host’s process manger, and the site (www.Velaction.com) serves up slow even when there are no process running. (It shows the php, but not the queries, though).

There’s no consistency in my error logs–some are from plugins, and some are from the core.
(example)
# Mon Jun 28 09:05:46 2010
# Query_time: 6.922412 Lock_time: 1.785105 Rows_sent: 646 Rows_examined: 748
use DBname_wp02;
SELECT option_name, option_value FROM wp_options WHERE autoload = ‘yes’

On a bad hour, I might get a few hundred erros. In the afternoon, I might get none, or one from a related posts query.

In the slow times, I tend to get clusters of errors, presumably from several queries on the same page being run. Most of my pages generate between 30 and 40 queries with the plugins I have.

Speaking of plugins, I’ve tried disabling them (or all the ones that don’t break the site when I turn them off), and there is no difference. I’ve also optimized and repaired my database.

I couldn’t find any link between something I installed and the slowdown–just started happening.

Again, I don’t get the volume of traffic that I would expect to make this a problem.

By the way–I’m pretty much a hack, mostly copying code and doing a few basic tweaks. It’s possible I put some bad code somewhere, but I don’t know why the same page would load 10 times faster in the afternoon if that was the case.

Any ideas?
Thanks
Jeff