Oh right forgot about the timeouts. Most hosts won't let you change it. That is unless your own your own dedicated server. If your on shared or reseller, then most likely no they wont allow it.
Well what you could do is is use phpmyadmin. And delete old threads and limit it to sections. So maybe delete 10,000 at a time or less. I don't know if phpmyadmin has a timeout limit as well.
Then to fix things you could rebuild the thread indexes to optimize.
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