The Motor Control Problem resolved! ( interns of calibration and successful machine move ) ( But I still need your valuable help on bed calibration Should I open a new thread?)
Thank you very much for all your contribution.
Solution: I have just upgraded to the latest beta Firmware and DWC.
Conclusion:
But the configuration remains as (P 2-3-4) I was using. The recommended P 5-6-7-8 values causing problems. If it is not an issue with "Duet 2 Wifi r.104" It is something with the firmware I believe.
The Problem with recommended configuration P-values causing missing steps and noisy move. Each axis even the same amount moves command, they move different distances.
By the accidentally found settings and new Firmware update problem is over!
So this is the code that is working so far:
; Drives
M569 P5 S0 R0 T3:3:5:0; Extruder drive 0 goes Forward
M569 P2 S1 R0 T2.5:2.5:6:6; X: A drive 1 goes Forward
M569 P3 S1 R0 T2.5:2.5:6:6; Y: B drive 2 goes Forward
M569 P4 S1 R0 T2.5:2.5:6:6; Z: C physical drive 3 goes Forward
M584 X6 Y7 Z8 E5; set drive mapping
M350 X1 Y1 Z1 E1 I1; configure microstepping without interpolation
M92 X114.29 Y114.29 Z114.29 E274.00 ; set steps per mm (400/140) * 40 = 114.2857 ;; 400 step per rev ;; 140 mm one rev pulley ;;1:40 ratio gearbox