Re: missing steps.
About the Z axis-
I noticed in the background of one of your pictures that your Z rod doesn't use an ABS coupling to attach to the motor like mine, which should be good because it wouldn't be as prone to wobble. How is it mounted to the motor? It looks like the threads stop short of the motor. Does there seem to be a flat on the bottom of the rod, or does the mounting somehow rely on friction against a round rod?
I wonder if there is a way for slippage to occur there, so that sometimes when the motor turns, the rod doesn't. That would certainly cause the kind of squished layers you are seeing. You could try stepping the platform down in .3mm steps and watch the rod to see if it turns every time.
Home the Z axis. Under the log window, there is a text box with a send button for manually sending gcode commands.
Send G91 to enable relative coordinates
Send G1 Z.03 to move down .3mm. It will send the same command again every time you hit the button, so keep clicking it to keep stepping the platform down, watching for the rod to turn each time.
You could also run it all the way up and down in a single motion and see if you can hear anything that sounds like skipping or strain, maybe hold a finger against the bottom of the rod to feel for any catching or odd vibration.
