I didn't understand why do you need the last space vectors with you already have the transformation matrix.
If you are trying to do a space transformation from R^n to R^m you just need a m x n matrix and to multiply this matrix to a column vector in R^n.
In your case, you can write:
A= [0.3898 -0.0910 0.9164; 0.6392 0.7431 -0.1981; -0.6629 0.6630 0.3478];
P = [ [x'1;y'1;z'1] [x'2;y'2;z'2] ... ] % The idea is that you need column vectors of x,y and z.
and just P_R3 = A*P;
I believe that this can solve your problem.
