I don't think there is an Adpatation procedure for the EDK. The adaptation is automatic.

Here's what I found about ther M62 TU engine and the EDK.

The EDK is continuously monitored during all phases of engine operation. It is also
briefly activated when KL 15 is initially switched on as a “pre-flight check” to verify it’s
mechanical integrity (no binding, appropriate return spring tension) by monitoring the
motor control amperage and the reaction speed of the EDK feedback potentiometers.
If faults are detected the EDK motor is switched off and fuel injection cut off is activated
(no failsafe operation possible). The engine does however continue to run extremely
rough at idle speed.

Since you have fault codes if the fuel injection cut off is activated that may be the reason why the engine dies. If you clear the fault codes and start the engine, the EDK maybe able to adapt to the new throttle pedal you installed.

Why did you replace so many parts in the first place? Also a new DME requires adaptation to the flywheel.
Here's the complete write up on the M62TU

http://www.e38.org/m62tu.pdf