Another weekend passed and I've spent it being frustrated.
at first I've tried fixing the Z axis and adding smooth rods instead of the previous piece of wood.
and then passed to motor calibration.
for some reason I've noticed that when the motors move to one direction they move faster that the other way around.
Google searching the issue suggested that that may occur because the endstops were not installed.
I've tried connecting one endstop and checked it is working by clicking the mechanical switch - and then the Arduino restarted -weird.
I've checked and found out I've switched pins in the endstop connection and switch them back.
But then it occurred to me that the LCD was in full brightness so I couldn't see if it is running or not, and the repetier software couldn't find the arduino through USB.
when removing the Ramps 12V input I've noticed that the LCD was back to normal and I could control the UI, and whe I've reconnected the 12V and the brightness was full again I could notice you can barely see the UI still operating.
I've decided to disconnect the Arduino Mega 2560 R3 board and fix it first - and made a total mess.
I've managed to get the board unrecognized when connected to the PC USB, probably by deleting the bootloader somehow.
I've found a similar case online here.
for now I think the Arduino board gone bad for one of the two reasons:
1.software corrupted.
2. burned chip on the board.
I've ordered a new USBASP in order to maybe fixing the board bootloader and 16u2 USB serial connection chip firmware.
also bought a new Arduino Mega 2560 R3 in case that will fail. I will be able to sell it if I'll fail to fix.
This will delay the build for a while...
When I've decided to build the printer alone and with no kit I knew that it will be harder and have setbacks like this, but when it really happens it is still very frustrating.
now all I can do is wait for a while...