Database clean up generates 503

I’ve been working on a site with hundreds of thousands of stats records. Upon cleaning them the site slows dramatically and I get hit with a 503 Service Unavailable.

The most common cause of this problem is that your computer at IP address xx.xx.xx.xx has opened too many simultaneous connections to scripts on this site.

I don’t do much with queries & db but I imagine there might be a more efficient way?
I have a video in drop box showing the issue and how long it took to reset the link data. Let me know where I can email that too. (not asking for support on this, just thought it might be useful & a good improvement)

Thanks! 🙂