There is more to it than just changing the connection string. We have a separate package for SQLite that has different data dls and different database scripts. If you want to use SQLite then you need to install the SQLite package of mojoPortal.
My recommendation is if you want a file based database, then use the new SQL CE package for mojoPortal, it has better performance than SQLite and can be migrated back t SQL server if traffic outgrows SQL CE capacity.
Hope it helps,
Joe