Up to now I have failed to flash at any speed above 10400 baud, this meant 12 minutes to flash a 1Mb file.
However, since monoscan suggested these settings
http://sites.google.com/site/monoscanen/how-do-i-configure-the-ftdi-driver, I tried it with Nefmoto and now it connects at maximum baud and flashes in 3 minutes. I am very pleased indeed.
I think the key is reducing the latency to 4ms.
My ECU is 06A906032HN.