To answer your question about the Good set, yes, renaming the extensions of the actual cartridge dumps to .j64 will work (this will NOT work for demos and other homebrew programs).
Currently vj doesn't look at the config file to find paths for a ROM passed in on the command line (it should). Supplying the full path works as long as you do it right. For example, if you have a ROMs subdirectory with a zipped ROM named foo.zip, you would say
Code:
vj ".\ROMs\foo.zip"
for VJ to find the ROM.
When you run VJ, does it create a stdout.txt, stderr.txt or a vj.log file in the same directory where VJ lives? It should.