Which db is used is determined only by which version of the data dlls you have in your bin folder. You must have the MySql version of mojoPortal.Data.dll (and possibly mojoPortal.Features.Data.dll and WebStore.Data.dll) in your bin folder,maybe you followed the instructions in this post, but those instructions were for using MySql and therefore had the extra step about downloading the MySql data layer and replacing the files in the bin folder. That step is not needed for MS SQL.
The dlls for each db have the same names so only 1 possible version can be used at a time, it seems like you copied in the MySql version into your bin fodler before uploading. The ones included in mojoportal-2-2-7-3-mssqlreleasefiles.zip are correct for MS SQL.
So its not about configuration or references, its just about having the right dlls for the chosen db and then setting the connection string for that db. If you are seeing that same error then you definitely must have the MySql dlls.
Hope it helps,