So, you have programmer, that connected to mainbiard through keyboard connector?
You need something like this to flash EC directly.
I’ve got a ch431A programmer and use it with another computer with a clip and can program it directly no problem. Just don’t have the dump
Are you know how EC looks like? 
With this programmer you can flash only SPI and some EC (kb90xx).
I’ve got the correct chip. It fits on the clip fine. And I’ve been able to read the contents of the chip. But I have had trouble flashing it.