3D Printing Calibration - How to adjust the steps per unit for X-axis, Y-axis, Z-axis in Marlin Firmware

I recently 3D printed an enclosure for a project and there are several obvious issues with the print.

Environment:

Marlin Firmware Version: V1.1.0.
Filament: Clear PETG
3D Printer: DIY Prusa i3 type 3D Printer

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The issues:

1. The height of the openings (for RJ-11 sockets, USB, Power Socket, etc.) of the enclosure is smaller than my design

2. The extruder head scratches the surface (the bottom of the enclosure) of the printed layer while printing it

3. There are traces of extruded filament across the openings

4. There are visible dark spots on the printed surface

Solution to issue no. 1 & issue no. 2

I suspect the issue is caused by the Z-axis not travelling enough distance. So I measured the dimensions of the print and adjust the steps per unit for the Z-axis. At the same time, I took the liberty to adjust the figures for the X and Y axis as well.

Note,

After testing, it seems using 4656.6 is not enough (the nozzle still scratch on the printed layer). Need to try 4736 (3980 x 1.19) and see if this will solve the problem..

Note, 
Be sure to upload the Marlin firmware with the modified "Configuration.h" file to the 3D printer control board!!

Reference: 

3D PRINTING: Calibrating your Z height
https://www.youtube.com/watch?v=qEaA3kU__Mo

Solution to issue no. 3

The original retraction settings was 2mm for Length and 40mm/s for Speed. I changed them to 12mm and 80mm/s respectively.

Note, 

DO NOT set the retracted length too long, otherwise the filament may jam between the extruder nozzle and the heat sink block. For my E3D v6, 20mm seems too long and will cause the jam, 12mm seems O.K.

Reference:

Stop the stringing with Retraction! 3D Printing 101
https://youtu.be/XZTBSJAswbs

Solution to issue no. 4

I suspect this issue shares the same cause as issue no. 1 and no. 2. Because the nozzle is too close to the printed layer (z-axis not moving high enough), it causes some of the filament to build up and cooked inside the nozzle, and this filament spills out from the nozzle during layer change.

It's yet to be tested to see whether this issue will go away as the z-axis travel distance is now moving at expected.

Testing out the changes

After the Marlin firmware is modified and uploaded, print a test cube to check the result.

I have created a test cube for testing. You are welcome to download it and test it out.
https://www.dropbox.com/s/q5z9j0yeugu89b5/Test_Cube_30x30x30.stl?dl=0

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IMPORTANT!!

Make sure the Z_PROBE_OFFSET_FROM_EXTRUDER is corrected set before uploading the Marlin firmware. For my DIY Prusa i3 style 3D printer with 30 x 30 x 30 printing envelop and E3D v6 hotend and auto bed leveling done with servo motor, the figure is around "-7.2".

When setting "Z_PROBE_OFFSET_FROM_EXTRUDER", the 3D printed result should be like the one on the left side in the photo below. The one on the right side needs to have its nozzle lowered by another 0.5 ~ 0.7 unit (ex., if it's -7, then it needs to be changed to -7.5 or -7.7).