Green is ground in Hondaspeak, so if you used the green wire in any combination and tried the flasher, you sent power to ground which blew the fuse. That wire is unused. The black and the grey are used on the flasher. I do not think it matters which position they're in, but it should work one way or the other with no harm done.
More commonly the problem lay in the grounding of the turnsignals - they ground through their bases to a lug that then connects to the wiring harness green wire. I went through this in my build thread in some detail (look in my signature for a link)
What led up to them not working?
The flasher is probably fine, just connect up the black and gray in either position and try again.