Im sure most people have stopped looking at this forum now but its worth a shot still.
I did have my printer running ok ish. i made some upgrades to the linear rails to make it run smoother. after putting the printer back together and recalibrating everything as per the set up guides. the printer still trys to print the first layer too high. about 0.5mm too high. i have managed one or two prints but putting an extra manual offset before printing but this isnt actaully fixing the issue.
i have tried recalibrating the z offset about 10 different times and still the same issue. has anyone had this problem and managed to correct it?
i dont think it is a mechanical issue as i replaced the stepper motor with the one i used for the 2nd extruder. So it must either be with th slicer or marlin. however the G.code looks fine to me. and i havent made any changes to marlin sinse the original set up.
There is a Z_PROBE_LOW_POINT setting in the firmware (configuration.h) that was also changed by makertech3d a while ago. I'm not completely sure about this, but if I understand it correctly, it limits the maximum range of the Z-probing from the printer's original z=0.0 point. If that's the case, it might limit probing into the bed when auto-leveling. It's currently at 3mm which should be sufficient if you follow the procedure from the build manual when mounting the z-probe sensor (resulting in about 1mm distance between sensor and hotend). It might fail when the sensor is mounted too high.
I had the problem of 'printing the first layer in the air' several times after calibrating and fixing the printer. As I assume meanwhile, it has to do with the distance between probe and nozzle. I guess when it's more than a millimeter, the Z-Offset does not compensate it.
For me, increasing the number of measurement points for the bed leveling and then turning on babystepping and really dialing in the Z-Offsite through the Tune menu while printing, I've been able to get the first layer working well.
Both of those things are in the configuration.h Marlin firmware.