I actually figured out the answer. So like I said the R matrix is of the size 2fx3 and I was confused how that corresponded to a normal 3x3 rotation matrix. So it turns out that since R is stacked such that you have
r1x
r2x
r3x
r1y
r2y
r3y
Where each row is a 1x3 vector that corresponds to a row in a normal rotation matrix to get the rotation from the initial points to the new ones you take the corresponding r rows for x,y and cross them for z. So to get the rotation matrix for the 1st frame it would be (each of these is a 1x3 vector)
r1x
r1y
cross(r1x, r1y)