The Cat is worse than the muffler, especially aged Cats, on second generation diesels.
There is no point in an intake. The only thing you stand a chance of gaining is MAF problems. The stock intake is the best combination of filtration efficiency, freedom, and code free operation that exists. The aftermarket intakes are a complete waste of money, unless you need to run over 70 lb/hr airflow. That is over 32 psi at 3400 rpm. And no box tuner does that really. Eliminating heat soak in the intake is another matter. That is the worst offense, not restriction. Airbox temps of over 200 degrees. And AFE/KN does not help with that.
A V-clamp back exhaust is definately an improvement, or splicing as mentioned earlier, and improvement to egt. The downpipe restriction is significant, but these restrictions are in series, eliminating a lesser restriction does not negate its benefit, just because there is another restriction that is even more. The garden hose idea mentioned proves this. 2 equal length hoses, a 1/2" and 3/4" hose. Put a 1/2 id" washer in each one, and the 3/4" hose still flows more, with less total pressure drop, a fact.