MySQL, anyone?

I need a little bit of help from a MySQL-savvy person, so please forgive me the technical mumbo-jumbo following below.

The database update which is necessary for the Antville 1.2 upgrade takes long. Very long. Too long. I started it yesterday at 1:30 in the night and it is still running.

Well, you might say, haven't you written the update script yourself? Aren't you the guy who should know why it's running so slowly?

But I am really pretty clueless right now. Because all I am doing is issueing quite simple select, update and insert statements.

The problem might be, though, that it's Millions of them. During the first few hours everything goes quite smoothly, but after that each bulk of inserts or updates to a table (especially the one containing all the lovely postings of the Antville.org community) is interrupted with a break of a few minutes at first which in the meantime even exceeds ten minutes.

Thus, the update is taking longer and longer and longer. And of course I don't want Antville.org to be down for such a long time.

I already tried different things I found on various websites and in the depths of the MySQL documentation, even with some success in speeding up things a little bit.

But it's still not working out...

So my urgent request is: if you know how to optimize MySQL performance pretty good or you know someone else who does, please please please get in touch with me as soon as possible.