Sorry guys, I'm going through a rough patch right now.

For the facelifted e53 (or 6HP tranny), use/select EGS in SSSProgman. There is no GKE "scripted" in the software. The SIB refers to it as: "EGS/GKE" so it's clear the mechatronic module is referred to (GKE) and not transmission module (EGS).

When programming, have the power supply attached to the +/- under the hood. Make sure the battery is fully charged prior to this.
During the programming be patient. There will be moments when it would seem like nothing is going on, or the clock (counter) would go the opposite way. It's normal. Just tough it out and wait. I know, you can start questioning yourself during that stage. Patience is a virtue. And Progman pretty much guides you through the process.

Once the re-flash (programming) is successful, you have to perform the 1-2 tip-in procedure, like this:
Start the car, and drive at moderate speed. While driving (a quiet residential area is the best), come 5-6 times to a stop. Every time you stop, MAKE SURE you perform a FULL STOP. COUNT TO 5, then start driving again. After 5-6 full stops, park the car, and let sit for 1/2 hour. Done.

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Stable: e92is, e46 M54B25, e83 N52, e53 N62 - sold, e39 M54B30 R.I.P.