As you note, ArcGIS 9.4 uses GDAL 1.6. Consequently, to make your GDAL driver work in 9.4, you will have to recompile your source code with the GDAL 1.6 include files and stub library. A new GDAL driver sample for 9.4 includes the files for GDAL 1.6, and will be posted to the code gallery soon. It also discusses some new ways to support custom geotransforms in ArcGIS 9.4.
We are in the process of posting these files, but I don't know exactly when they'll be available.