What engine? I can't be absolutely certain, but I think the j-pipes in my kit were dang near the same length. If anything, I'm guessing that the passenger side was a tad longer...? I'm using a modular 4.6 motor.
If the length is significantly different, just mock up the j-pipes and see which sides they make sense on. The sidepipes are very nearly identical (or mine were), so you'll want a j-pipe to reach each side of the car roughly equally, if that makes sense.
Cheers, John