Have you actually tried CapSPC? It supports MIDI converting from Goof Troop, since it's a Capcom game. Unlike NintSPC it doesn't convert to MML though.
P.S. You only have to set the instruments on your own.
logall.bat / convall.bat are found in the misc folder and to be copied in the bin folder where capspc.exe is located. Usage pretty similar to NintSPC.