I used ExInjector to inject it back into the rebuilt rom. (decrypt exheader file first of coarse.

) That might help. Did you try that? The resulting exheader file is 2KB in size compared to the 1KB in size that when extracted with 3DSExplorer. I don't use ctrtool for packing RomFS anymore. I use that RomFS Builder that SciresM/Kaphotics has now. That might also be a factor. But I believe it's the exheader.
My rom boots without the patch. Not sure why it didn't work for you. I didn't change much about the RSF file. So I'm sure it was just the exHeader extract/inject method I used that fixed it...