Building the i3 mk2s - strange things happening: while the Y stage is level on all 4 feet, when I attach the Z plate and fasten it to the threaded rods it all gets squeued and i have a leg in the air again. Moreover, it seems to tilt around the plate foots’ line. I have also checked the squareness of the undercarriage with the upright Z plate … and it’s also off a bit… it’s already frustrating 
The carriage could be warped, causing the bearings to bend the y rods. Upgrade to 10 or 12mm rods would probably fix this.
Ok, I took it apart again, detached the Y assembly from Z, loosened the Y belt (I believe tight belts can skew Y platform after all) and placed two flat boards just under the foots of the printer (Z plate wasn’t touching ground). Then I made undercarriage square with the Z plate which meant fastening a bit more one Y rod to the Z plate and tapped up and down the Z plate on the other side until it was flush with the square. Quite happy now 
@Stephanie_A I do’t think the carriage is warped cause without the Z plate it stayed on all 4 feet flush with the table. I came to believe that the Z plate shouldn’t touch the ground at all, which it did before. Basically I played with the Z plate tilt in plane to get it perpendicular with the undercarriage.
The z plate does not touch the ground (or table). That tripped me up as well. Keeping the z plate attachment to the y rods at precisely 100mm from the back corner in each side was also tricky.