Sturm, you say this is a database issue at its heart.
That doesn't surprise me. You're using MySql, which costs what? Free. Any of you there ever hear ye old "You get what you pay for" axiom? MySql is great for kiddies, students on a budget, and novice programmers getting their feet wet, but if you went into this thing thinking you had an enterprise-class computing stack, you got sold a bill of goods.
I could help you migrate to a better, more robust, powerful, scalable solution, with massive uptime improvements to boot, but it would cost you. I guarantee you, though, that my fees ($120K a year, + hardware + software + 120,000 RP a year) are CHEAP compared to the amount of money you lost *this week alone.*
Contact me @ clary dot david at gmail. Let's talk. If you're ready for a real database that gives you the kind of power, reliability and performance you've actually promised your customers, you're ready to get the hell away from MySql.
Oh, and everyone else not working at riot? Go read my webcomic. It's hilarious. My mom totally says so.