I tried to change the EM406 back to NMEA through sirfdemo but with no success.
Anyway, saw in another forum a message mentioning that everything fails you
could switch it back to NMEA by disconnecting the power and waiting for
3 days.
Doing that worked in my case. The first try after that worked as expected,
with the NMEA messages coming at 4800 bps.
At least for my case, monitoring the serial traffic using the Tx and Rx Arduino
pins was possible with no need to any level conversion. It was simply a matter
of connecting the right pins.
Thanks again for all that replied.