I work in product development at CO2meter.com, So I can certainly help you with the sensor part. Co2 meters come in several different ranges. Depending on what range you think you will need, I would recommend our Cozir Rh/T http://www.co2meter.com/collections/co2-sensors/products/cozir-0-2-co2-sensor
. It comes in 3 ranges up to 10,000 ppm (For a point of reference, ambient atmosphere is around 400-450ppm), and incorporates humidity and temperature.
This particular unit works over UART and has a very simple interface. I have written a small library for it to work with ARM processors, but I can definitely help you get it running on an arduino. Assuming you still want to use the arduinos ftdi to report back to a host computer, this will take 2 pins to run a software serial connection.
for the stepper motor control you can use 4 control boards like this : http://www.pololu.com/catalog/product/2128
. Each board requires 2 pins from the arduino, but if you are sure you will only need to run one motor at a time, you should be able to use one pin for the DIR signal on all 4 boards. So this would only take 5 pins.
each of the servos, and simple on/off devices will require 1 pin from the arduino, so this is certainly possible with a basic arduino. However it is a good idea to leave some room for re-design and expansion, so I would use a shift register for the simple on/off devices. If you are new to shift registers, it is basically just a way of expanding your i/o pins cheaply. I did a quick tutorial on my personal site a while back: http://girshwin.com/led_shift.php
If I were doing this project I would probably get a proto-board big enough for all of the sub-assemblies and attach an arduino micro/mini to it. Then I would breadboard each part with the arduino that you already have and make sure its working before attaching it to the protoboard. It can be pretty easy to overheat/damage a stepper controller sometimes, so I would definitely use headers to attach them so you can change them out if needed.
*Note: when working with the stepper motor boards, if you need to adjust wiring make sure to turn off the power first. Disconnecting and reconnecting motor leads while connected to power can damage the stepper board.