FJ62 Cat Replacement Fitment Issue

[wrc3]

So I am replacing the driver's side cat on my 1990 with a "direct fit" from Rockauto.com. It appears to be an Eastern Cat. Anyways after removing the old cat I noticed that the pipe and flange on the down pipe from the engine are not flush. The pipe extends maybe 1/4 inch past the flange. This is also true of the pipe leaving the cat that goes on to the Y and muffler. The old cat left room for this extension by insetting the pipe from the flange on the cat, but the new cat does not. Should I cut the pipe down to be flush with the flange and then mate it up with cat or is the new cat I have not correct? It looks correct in every other aspect except this.

B

 

[wrc3]

I know it sounds confusing, but it isnt really. Its just that the flanges from the cat and the flanges from the pipes dont mesh together because too much pipe is stick out of the exhaust side pipes.

 

[wrc3]

Nobody ever ran into this replacing their cats on a 62?