The following issues are un-resolved:

It is curious in this approach that the system is not aware of the version so that it can appropriately run the upgrades.  So, to avoid the mess I began with, deleting the scripts from the schemaupgradescripts directory up to the same version number that was in setup enabled the install script found using setup/default.aspx to operate as expected. My belief is that this deletion process shouldn't be required, since the script should be aware of what version it ran to begin with and would incrementally begin at the next number in sequence.

 If the first script had succeeded the .NET code would have inserted the version information into the mp_SchemaVersion table and then it would have known the next script to run is higher than 2.2.7.8

if the mp_Sites table exists it assumes an upgrade instead of a clean install. So the first script created the mp_Sites table but then failed, so when setup ran next it detected the existence of the mp_Sites table and decided it needed an upgrade not a new install. Since the mp_SchemaVersion table did not have the version info (or perhaps was failed to create that table) then it tried to run upgrade scripts and it ran old ones because they exist and as far as it knew were newer than the current version since version was not known from the db.

I hope the 5.2.5 version of MySql connector will solve this. The fact that scripts run from query browser shows there is no error in the scripts.

Best,

Joe