Hi Geomancer,
. . . Now I understand. Like Kef, I was confused by the first post.
It sounds like you wish to program the FPGA to emulate one of the CodeWarrior supported BDM interfaces. That's no small undertaking.
Except for the USBDM and the OSBDM (which is now obsolete), I know of no documentation for the inner-workings of the debugging interfaces. I am not familiar with any serial-port based interfaces either, as they seem to be all USB based now. So it is likely that you would need a USB interface as well, either internal or external to the FPGA.
If you look at the USBDM firmware, which is open-source, you can get an idea of what you would need to implement. I suspect that all prior BDM interfaces have been firmware-based, so coding it in an FPGA may need a considerable amount of resources. As FPGAs are not cheap, it may end up being an expensive way to go. I realize that you already have the FPGA on the board, but I suspect a debugging interface would require you to go to the next larger size (if it fits at all).
I would suggest just putting the M9S08JS16 on the board and using the standard USBDM firmware. That will give you a supported debugging interface with the USB interface on-chip. I think it would be a lot simpler and cheaper than trying to put all of that BDM firmware into an FPGA.
However, if there was documentation on writing a debugging driver for CodeWarrior, or even an existing low-level driver, then it might be a different story.