In case this helps the next guy... (this is only my opinion, your mileage may vary, etc)
The PSTCLK on the BDM connector may be a significant source of emissions at 120MHz (half the CPU clock) and it's harmonics. To turn this off in your shipping product (because turning it off earlier disables BDM debugging), you can execute the supervisor instruction WDEBUG, setting the proper bit in the CSR.
If you're using uCLinux and the LTIB, there's a convenient flag that can be set under kernel configuration, kernel hacking, to set CONFIG_BDM_DISABLE. It seems like this was intended to enable a bit of code in arch/m68knommu/platform/532x/config.c that will execute the proper WDEBUG command for you. The catch is that it seems as if somewhere along the lines, this used to be called MCF_BDM_DISABLE (in the version of the LTIB that I'm using...kernel 2.6.17.1). So to make the kernel configuration flag work, rename MCF_BDM_DISABLE to CONFIG_BDM_DISABLE in config.c, and rebuild the kernel. Voila! you've got a kernel configuration flag that you can set on your shipping code, and clear when you need to debug using the BDM.
