I have a 4 3-D-points, each of them has only 2 of 3 known coordinates, as follow (? is unknown here):
P5 (P5x, P5y?, P5z) P6 (P6x, P6y?, P6z) P3 (P3x, P3y, P3z?) P4 (P4x, P4y, P4z?)
They build together a rectangle P3-P4-P5-P6 as follow (blue lines have defined length, the length of yellow lines are to find):

How to find missed coordinates P5y, P6y, P3z and P4z?
We know $P_5P_6=P_3P_4$, so $P_{4z}-P_{3z}=P_{6z}-P_{5z}$ and $P_{4y}-P_{3y}=P_{6y}-P_{5y}$. As a check, we should have $P_{4x}-P_{3x}=P_{6x}-P_{5x}$.
We also know $P_5P_6$ is perpendicular to $P_3P_5$, so $$(P_{5x}-P_{3x})(P_{6x}-P_{5x})+(P_{5y}-P_{3y})(P_{6y}-P_{5y})+(P_{5z}-P_{3z})(P_{6z}-P_{5z})=0$$
That is only three equations in four unknowns, so you need one more equation.
I want to rewrite the equations without subscripts. $$P5(a,x,b), P6(a+c,x+f-e,b+d),P3(a+e,e,b+y), P4(a+c+e,f,b+d+y)$$ where $a$ to $f$ are known, but $x$ and $y$ are not. The last equation becomes $ce+(f-e)(e-x)+dy=0$. Pick any value for $x$, and then $y=(e-f)(e-x)-ce)/d$.