Given how the sides of your 'cubes' are dished, and the other dimension problems, it would seem most likely that there's an incorrect dimension somewhere. Just a guess - though the rods come with the length on them, you have a mix of mag balls and ball joints; does the rod length include the radius of the mag ball, or the additional length of the ball joint? It really would be worth checking length of an arm to the centres. Also check the delta radius has not changed with the change of the carriages (you say it hasn't, but still worth checking).
Ian