I'm not sure I understand the first part of your question, but if you want a transformation that carries one set of points to the other, here is a simple method to understand (though certainly not the most elegant). I will use the point sets you mentioned, A {1(87,159,28) 2(-97,216,15) 3(60,237,9)} and B {1´(96,6,35) 2´(-86,62,23) 3`(71,82,14)}.
I start with A
(87,159,28) (-97,216,15) (60,237,9)
and translate it to bring point 1 to the origin:
(0,0,0) (-184,57,-13) (-27,78,-19)
Then I rotate about the z-axis to bring point 2 to the x-z plane:
(0,0,0) (-192.6,0,-13) (-48.9,66.5,-19)
then about the y-axis to bring point 2 to the z-axis:
(0,0,0) (0,0,193.1) (-15.7,66.5,50.0)
finally about the z-axis again to bring point 3 to the x-z plane:
(0,0,0) (0,0,193.1) (-68.3,0,50.0)
These steps, taken in order, carry things from space A to a new space, call it C. Call this transformation Tca. These steps are reversible-- call the inverse transformation Tac. Now do the same with B to get Tcb and Tbc. The two sets of points will match when they are both in C. Now to carry set A to set B, just apply Tca and then Tbc. To go from set B to set A, apply Tcb then Tac.