I just constructed a Prusa Iteration 2 using an original Prusa threaded bar/rod kit. The only difference I noted was in the X-Carriage smooth rods. Instead of the 420mm rods used by the original, Iteration 2 required 400mm (.5" shorter). This is because the X End Idler and X End Motor are now push to fit instead of set screw adjusted.
The rods were easy enough to trim with a cut off wheel and smooth with a grinding wheel.
In summation: Replace 2 each 420mm smooth rods with 2 each 400mm smooth rods. Otherwise, use the original BOM.