Ha! PWM water pump control. [H]ard.
Sorry, can't answer your question. I just remember quickly reading your [H]ard forum posts.
I don't think it's going to be easy to translate to gerber without putting your schematic / board design into a more advanced editor, with gerber output.
I might be able to do it for you, or at least recreate your board in Eagle and you can output it to gerber. There's some quick tutorials instructions for it out there.
I've read lots of stuff on cutting. Something that small might be able to be cut on one of those large paper cutting machine. I use a dremel with a cut off bit myself. It wouldn't take too long to cut up small baords with the dremel, but the cut isn't perfectly straight, unless you're real good with it. I've heard people using jigsaws as well, but I have no experience with that.