I've been wrestling with a CD4E in this Mystique for a couple months now. (See my "saga" in this same forum)
When you say it happens only under braking conditions, that brings something I learned this week to mind. One of the five solenoids in the pack bolted to the front of your valve body controls the lock-up torque converter. (TCC, or the MLUS as ford used to call it) This solenoid will lock up your torque converter in a very narrow band when your throttle position and torque load are just about even and it can save you some gas. Well there is one signal that will unlock it immeadiately, the BOO or brake on-off switch. Here's a test you can do. While holding your accelerator steady and driving at say a steady 55mph, lightly tap your break pedal, your rpms should raise by 300 - 500 for a few seconds, then fall back to where they were. If this doesn't happen, tho BOO sognal is not getting to your PCM for the TCC equation. Of course the TCC solenoid could be bad, but that should give you a code, and trouble at other times than just breaking.
Hope this helps.

Greg