I followed Jon's instructions and was able to get UrJtag up and running on my Ubuntu partition pretty easily. I was missing a couple libraries that I was able to install using 'apt-get'. I then patched the source with Jon's patches and built the system. So far so good.

With the source code in hand, I decided to make a cable that connected to my Phytec board and see if I could toggle the pins of the MPC5200. I noticed that the JTAG/COP signals of the MPC5200 were brought out through the expansion bus to the patch field of the expansion card. So, I decided to use some wire 'sleeves' (wire with female receptacles on both ends) to connect my Jtag connector to the board.

Here is the mapping in case anybody else wants to do it this way:

This almost worked except there were two problems:

1. No Clock. The TCK signal on the Phytec Patch Field (12E) is not connected to the TCK signal on the Phytec Edge Connector (7). So, I had to route this one manually. Do do this, I simply used one of my 'clippy' wires to clip onto the signal at the Jtag cable and clip on to the signal at the edge connector. I disconnected the cable from the Patch Field (12E), of course. Not sure where the Patch Field signal (pin 12E) goes, but it doesn't go to the COP TCK signal.
2. No Reset. The RST signal was keeping the MPC5200 in reset all the time. So, the minute I hooked up pin 4E on the Patch Field, the CPU went into reset. To fix this, I just disconnected the RST signal. I suspect that this line requires a pull-up resistor to keep the CPU out of reset. However, I didn't try it.