First off, when I bought the car, the main cat had been cut out. I wired up the 5/6 ports to work off of the air pump. Now I'm in the process of converting the car back to stock, well almost.

The pre cat is clogged so I want to just cut it out and put a straight pipe in, but I want to put a new main cat back on, and run the 5/6 ports off the backpressure like normal, would just the main cat produce enough backpressure to activate the 5/6 ports.

If this is a dumb question, flame away.

 

It will work fine with the stock main cat in there. If your car is an S4 all you need is localized high pressure in the split air pipe which the obstruction of the matrix will generate. It is not necessary to have the pre and secondary cat since they are upstream of the split air pipe