Sportrak wrong Exhaust ??

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Recently bought my 1994 sportrak after driving it for a short while found it was blowing at the cat inlet I fitted a new cat,when doing so found that the outlet joint to the rear box was different to the front and was difficult to get both ends to line, up the pipe diameter of the rear pipe is smaller but the holes for the bolts line up.
The exhaust seems fairly new, I am guessing that the wrong back pipe has been fitted . Can any one help?