Your description of the problem does not make much sense.
Why would the number of serial ports have any relevance to a 3 D printer?
I don't think anyone would consider the extruders to be additional axes what you describe is a normal 3-axis printer.
AFAIK 3D printers with dual extruders are common. Have you looked on the RepRap Forum where they specialize in 3D printing.
...R