Its sad to hear that you stop using ispconfig. I dont meant that your problems were nonsense, just the explanation makes no sense who knows how ispconfig and a multiserver setup work internally. We could have helped you to resolve the issue within a short time but you did not ask for help and the findings that you posted above - a mysql issue caused by the poster of that issue - was really not related to your problem in any way. A multiserver system is a complex setup and while you thought that the problem was caused by deleting and recreating the site it could have been caused by something totally different. I see that regulary in my daily work as system admin that the things that users thought are causing a issue are often not even related and just a timely coincident or it was something else that tehy did and they tell me later "oh I did not know that this was related so I did not tell you...". ISPConfig is used on > 100 000 servers worldwide so you can rest assured that it works flawlessly and you can delete a site and create it again without any issues, this is even a part of the tests that we do regularily for the ispconfig development and releases.
Within a few hours of making the DNS standalone, manually configured, I got hits again. Strange, I'd say!
A website in ispconfig is not connected to the dns part in any way in the controlpanel, so if using a standalone dns helped, then your problem was likely a dns or network problem and not a problem with recreating the website. Also the slow connections that you decsribe indicate a network or routing problem, both can not be caused by recreating a website as this changes only the apache vhost configuration file and creates the site folders, not more or less.