Charles, your project sounds interesting. What are you going to do with it? (I'm not sure what a Fiber Optic Injector is) My shield uses the PWM pins on the Arduino, but you don't have to address the pins with PWM. A digitalWrite() high or low on those pins will function as you should expect, although possibly reversed.
I HIGHLY recommend using the opto-isolator and keeping the uC logic on the Vin side of the puck. (In fact you have to with this shield) The 5v REF on the pucks can only provide up to 20ma each and you can not combine them in parallel for more current. It's not enough to power the Arduino. I fried the 5v REF on two of my three pucks doing this. Also I've measured between the Vin- and the LED- and they are at different voltages, which varies with the LED current level. So you must not try to drive the CTL pin directly from the Arduino if the Arduino's GND is tied to the puck's Vin-. The opto-isolators allow you to do it without hurting anything. All of this is a primary reason I decided to design the shield - so people could use the pucks safely. The data sheet doesn't explain it very well.
Yes, the capacitors on the power input are important to keep the transient noise down. They help the power supply keep up with the switching of the pucks. And if you are powering the Arduino from the same source, they help reduce noise in the power feed. I've spec'd one 220uF 50V capacitor PER PUCK on the shield.
Shackscs, I'm ordering the boards from Gold Phoenix (http://www.goldphoenixpcb.biz/
), which is where BatchPCB (http://www.batchpcb.com/
) sends their panels for fabrication. If you want a prototype or just a few boards, go through BatchPCB. For a production run of tens up to thousands, go through Gold Phoenix.
I should be able to sell the PCBs at around $10-13 USD each, plus shipping. This is just for the PCB - does not include any of the electronics or parts. However, I'm gathering up the costs for the parts and will post it here.