Low power motor control

Hello,
I am trying to implement a multi-motor control system. I want to be able to control 5 low power (~100mA per) DC motors driving linear actuators and receive input from 5 linear encoders. I want to be able to control this system in real time from a host computer using a serial connection (I also have SPI and I2C connections available, but am not all that comfortable with them).

My plan right now would be to purchase 3 pololu motor control boards (Qik Dual Serial Motor Controller - ROB-09106 - SparkFun Electronics), daisy chain them together (sparkfun claims an almost unlimited number of them can be connected), and control them via the tx/rx digital I/O pins from an arduino UNO. My first question is does the UNO have two programmable serial ports or is the usb connection on the board that goes through the atmega8u2 only for programming the board? I would prefer to not have to jump up to a board powered by an atmega2560, but if the UNO only hase 1 available serial port that I can use for real time actuation I think I would need to switch boards.

Assuming for now that the UNO does have two viable serial connections, I can eliminate analog encoders because for the resolution that I want (~.1mm) there aren't single output analog encoders so I would need at least 10 analog lines. The standard for digital encoders seems to be A-quad-B outputs, but I'm a little confused about the outputs. I was under the impression that reading one of these would require only two digital I/O pins, but a number of the encoders ( for instance this one: https://docs.google.com/viewer?url=http://www.microesys.com/m2/pdf-MII/Mercury_II_1600-Data_Sheet.pdf) have both A,B and -A,-B lines. Do I need all four of these connections? There are a number of posts about rotary encoders which I believe work on a similar principle, and posts seem to indicate that only 2 pins are being used per encoder.

Does the system I described above seem workable? Should I be worried about other things like reading that many encoders simultaneously? The movement of the physical system is going to be extremely low speed, if that effects anything.

Thank you for taking the time to read about my thought process, and potentially offering some advice.

UNO has 1 serial port. 1 set of pins goes to/from the USB chip and direct out the board at 0/5V levels.
You can use Newsoftserial to add more.
You could always add a 2nd serial port via SPI connection to a UART such as MAX3100.
Or go to a Sanguino board with ATMege644 & dual hardware serial ports, more I/O lines, more memory.
www.moderndevice.com carries them