Fudge - you can check the thermocouple with a millivolt setting on your meter, and put heat on the end.
Here's a link - pdf, page 4, left side:
http://support.fluke.com/FInd-Sales/download/asset/2434064_6121_eng_b_w.pdfThat will eliminate the thermocouple. Usually, though, it works or it doesn't. It just provides voltage to keep the valve open, and it's an on/off thing. It sounds more like you are getting strange air flow, not allowing parts of the burner to light, all the time. And that seems to point away from the switch, as well.
You can go through the entire pdf, there's a lot of good troubleshooting in there.
When you try to light it, you might take a long lighter (like the BBQ type), and while holding the pilot, see if you can manually light the unlit portions of burner. If you can, then it's usually an air thing. If you can't, then it's a gas thing.
It's easier in person to troubleshoot, but this is where I would start.
Roger