I have a script that will convert a text file into a resource file, so that I can have multiple language support by having text files for different languages converted into
Unfortunately I don't think there's an easy way of doing this. Custom Build Tools only run from within VS.NET - they don't run when you build your project using MSBuild from the command line.
In general, if you have the choice of writing a build tool as a Customer Build Tool or an MSBuild Task then choose the MSBuild Task every time as these Tasks will run in VS.NET and from the command line.
The designer.cs files for resources are there to support your coding. They give you the strongly typed access into the resource file. So, as long as you create your culture invariant resources in VS.NET (and let it create the .designer.cs files) then adding additional language support later (additional .resx files) should work fine.
If, however, your text files are your primary resource files, and you're adding new resource strings into these text files first, then you'll need to find another way of generating .cs files that allow you to code against those resources. If you HAD to, generating the .designer.cs file yourself (or somethign similar) wouldn't be that difficult. Using CodeDom or T4 you could create the helper class, using an existing .designer.cs file as a template.