yes there is a difference, with the ecc system having the centre cat that mounts with flanges, whereas the non ecc ones are overfit joints, there is a way to get around it but i cant remember how i did it, i didnt need any welding either (i dont think)
your best bet would be to get a non ecc manifold and full system, (i have one with a bung welded in it for the 02 sensor)
your second best bet is to get a non ecc front pipe and weld it into the ecc front pipe so it will mate with a standard rear section.
your 3rd best bet is, go to the motor factors and look through there exhaust book, my factors could get the parts for the super s exhaust system.