Ok, now things are clearer. For the first part, the one that you use a table to keep the parameters, I think it would be best if you used the parameters system that Joomla provides for every extension. A good place to start is here
http://docs.joomla.org/Component_parametersRegarding the clean-up, you can instruct the Joomla installer via the XML file of your extension to run a post-install script that can take care of your problems. Please read the link I provided in my earlier posts.
Also, let's analyze the type of customers you have:
1) "old" customers, that already have the beta version. For them, you can prepare another package for your extension that does the upgrade with all the tweaks we have discussed about.
2) "new" customers, that install the new version. For them, just provide a normal package, one that doesn't check for updates and everything.
Hope the above helps.