what exactly is the unit with which you give these measurements? Is it thousands of an inch? If yes, the difference between 0.040″ and 0.060″ is 0.020″, that is 0.5 mm. Whether one would tolerate that depends on what standard you apply and your preference.
At the moment when you measured this, it seems that your jig shows that front numbers are higher than rear numbers, and left numbers lower than right numbers, which would show that Z Axis is slightly tilted backwards and slightly to the left. But for the difference between the values at different measuring positions, the different heights may be a result of play in your measurement setup or of the unevennes of your wasteboard, or differences in the height of the points were your machine’s feet are located.
What you are concerned about may not be a matter of trimming the perpendicularity of the Z Axis (“tramming the router”). Trimming this will mainly have effects only on which patterns appear when surfacing or on the accuracy of vertical walls in deep pockets that you mill.
I ask myself, if you are crazy about trimming Z perpendicularity up to the point of not having started to use your machine since two weeks, i.e. if you are at the step of checking the perpendicularity of the Z Axis in relation to the plane that is formed by X and Y, you already have to be sure that this plane, i.e. the mounting surface, is flat, wich means both coplanar and even. You can ensure the evenness with the surfacing process, but not the coplanarity and thus not the flatness.
Machine could be twisted
If you have twisting in your mounting surface, it is difficult to measure it this way, because the twist will twist the X Axis too. And then your router will tilt according to the twist when moving it from left to right.
It is important that before doing 1.) is to have 0.): Ensuring Coplanarity of the worksurface, or better said, at first coplanarity of the four machine’s feet. Coplanarity means that all four machine’s feet are on one plane, which means to avoid that one machine’s feet is higher than the others, or better said, that your tabletop is twisted.
Many people go crazy for adjusting the rectangularity (“squareness”) of the Onefinity CNC (rightly because the Onefinity CNC, as its main weakness, does not ensure the rectangularity by itself) but they forget the crucial importance of coplanarity of the mounting surface.
Also many people believe that irregularities in their wasteboard will be eliminated with surfacing the wasteboard with a surfacing bit. But this is not true. If your machine’s mounting surface is twisted, i.e. if one of the machine’s feet is higher than the others, then your wasteboard will remain twisted, and so will every workpiece’s surface be twisted after processing.
To ensure coplanarity, Tom @TMToronto mentioned the fishing line method here the other day, which is simple and very accurate. Other methods are winding sticks, water tube level and level (optical instrument).
I would ensure this as the first step before assembling the Onefinity CNC on a table. Especially if your table has no diagonals to prevent twisting. This would mean that the coplanarity of your worktop depends on the evenness of the floor and, even after tabletop trimming, the coplanarity will go down the drain if you move the table somewhere else.