The JTAG port is used to flash the CP firmware. It has little to do with the majority of the functionality on the chumby.

If you want to reflash the kernel image, the quickest way to do it is to take the zImage file, zip it, and copy it to a VFAT formatted USB disk, and put it in a directory called "update2" by the name of k1.bin.zip. Even though zImage is already compressed, you need to zip it again because of the way the firmware updater works.

Then, power on the chumby while pressing the touchscreen, and continue pressing it until you get into special options. Select the menu option to update the chumby, and then select update via USB. This will take the kernel image on the USB disk and flash it into the device.

You can completely destroy the k1.bin.zip image and recover from this, because this update mechanism uses its own copy of the kernel that is unaffected by the update to k1.bin.zip.

If you want to add more apps, you need to build a cramfs filesystem, and use a similar procedure but name the resulting cramfs binary image rfs1.bin.zip, also stuck in the update2/ directory on the USB drive.

Hope that helps!