Typical V1 build uses 16T pulleys at 16X microstepping, on a 1.8° per step motor, for 100 steps/mm.
Changing your steps/mm to 100.358 will make the difference.
Before you do that:
Make sure that you are measuring the actual machine movement. For the Y axis, measure from the edge of the table to a fixed point on the Y plate before and after the move. For the X axis I would suggest that you measure from the edge of the core (Or plate on a LR2) to the YZ plate before and after. If you measure the length of a cut, or size of a piece cut out, you have to take the endmill diameter into consideration.
So if you had a 14" endmill, and you tell it to cut a square:
G92 X0 Y0 Z0
G1 Z-1 F180
G1 X1400 F1800
G1 Y1400 F1800
G1 X0 F1800
G1 Y0 F1800
G0 Z3 F360
Although it looks like this should make a 1400mm square, the reality is that you should end up with a 1393.65mm square, because of the kerf of the 1/4" endmill.
If you are measuring actual machine movement, and it’s still out by this much
Ensure that there isn’t excess slack in the belts. Tighten them up a bit, and it might make the difference.
0.358% isn’t that large an error. You might never notice this on a 3D printer, for example. Maybe your batch of belt was just off? Or maybe your batch of 16T pulleys? So long as it’s consistent, it’s fixable though by altering the steps/mm. I would be correcting this if it were my machine for certain, (And probably getting obsessive over making sure that the error is consistent.)
So… Make sure that the error is consistent. when measuring your fixed points, maybe break down that 1400mm move into 5 moves of 280mm each, which should show individual errors of 1mm each. I’d probably also do the cam for a bunch of smaller squares and use the calipers to detect smaller errors to be sure that they don’t change for small increments.
Edit: Squaring the machine is done with the
M666 command, which sets up an offset for the 2 Y endstops. (And 2 Z endstops for levelling the LR.) I can’t really help with specifics on the command usage, but it takes the argument of the axis and an amount eg: