All that was in 4.0's machine.config file was
<add name="Microsoft SQL Server Compact Data Provider" invariant="System.Data.SqlServerCe.3.5" description=".NET Framework Data Provider for Microsoft SQL Server Compact" type="System.Data.SqlServerCe.SqlCeProviderFactory, System.Data.SqlServerCe, Version=3.5.0.0, Culture=neutral, PublicKeyToken=89845dcd8080cc91"/>
So I copied the following from the machine.config file in the v2.0.50727 folder to 4.0's machine.config file.
<add name="IBM DB2 .NET Data Provider" invariant="IBM.Data.DB2" description="IBM DB2 Data Provider for .NET Framework 2.0" type="IBM.Data.DB2.DB2Factory, IBM.Data.DB2, Version=9.0.0.2, Culture=neutral, PublicKeyToken=7c307b91aa13d208" />
<add name="IBM Informix .NET Data Provider" invariant="IBM.Data.Informix" description="IBM Informix Data Provider for .NET Framework 2.0" type="IBM.Data.Informix.IfxFactory, IBM.Data.Informix, Version=9.0.0.2, Culture=neutral, PublicKeyToken=7c307b91aa13d208" />
<add name="IBM DB2 .NET Data Provider 9.7.0" invariant="IBM.Data.DB2.9.7.0" description="IBM DB2 Data Provider 9.7.0 for .NET Framework 2.0" type="IBM.Data.DB2.DB2Factory, IBM.Data.DB2.9.7.0, Version=9.7.0.2, Culture=neutral, PublicKeyToken=7c307b91aa13d208" />
<add name="IBM Informix .NET Data Provider 9.7.0" invariant="IBM.Data.Informix.9.7.0" description="IBM Informix Data Provider 9.7.0 for .NET Framework 2.0" type="IBM.Data.Informix.IfxFactory, IBM.Data.Informix.9.7.0, Version=9.7.0.2, Culture=neutral, PublicKeyToken=7c307b91aa13d208" />
I then ran LLBLGen Pro 3.1 using the force .Net 4.0 link and was able to connect to the database successfullly. Thanks Frans!!