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> I am still looking for a way to use the version of SQLite that I choose with C# or VB.NET or VBA or R.

Short answer: build your own binary of C#/VB.NET/R wrapper DLL and link it with the version of SQLite of your choosing.

If you are lucky enough and the wrapper uses dynamic linking, you may get away with only building your own SQLite DLL (we might help with that!) and replacing it in the appropriate directory (somewhere near the DLL for C#/VB.NET / somewhere in `.libPaths()` for R). The fact that it's hard and requires some knowledge of the innards of the target language infrastructure to build your own version of C#/VB.NET/R/whatever other language wrapper  is unfortunate, but unavoidable.

For example, with R you might have to download the source code of the package providing you SQLite, replace the bundled copy of `sqlite3.c`, then run `R CMD build path/to/source/directory`, then `R CMD INSTALL` the resulting rebuilt copy of the source package (which requires installing Rtools on Windows). You'll probably get better help in the R-help mailing list with that, because it's R-specific, not SQLite-specific.