I had a feeling Chris needed more than just generic advice.
Okay, Chris, I'm going to vote for the very first thing you asked about, not the PWM Controller you have now, but the one on Ebay, that you first mentioned and I also have, and that I have connected to an ATX PSU, which you also have and seem to be familiar with. And I have run it with a windscreen motor.
Now, since this outfit has already been tested with a windscreen motor, since it is cheap, and uses your available parts, and you only have to buy one thing, that controller, as opposed to a bunch of things -- transformers, rectifiers, capacitors, it's easier and doesn't require building something.
Also, since the pwm controller you have now isn't satisfactory, put it on the shelf for some other purpose, or return it for more than the Ebay one costs, and smile all the way to the bank!
Now if you do this, please make sure that your ATX power supply has at least 8 amps available on the +12 output, and you will need to do a couple thngs to it to make sure it comes on, and has a load on the 5 volt line, as someone else mentioned earlier. But that's not hard to do. And we can help with that.