Op, you have an issue you want to fix but, you also want to do some upgrades. Fair enough but, fix the problem at hand first, then go after upgrades. You are assuming that the Cats are the problem but, what if they're not?
With so many variables thrown into the mix (new parts, new tune, etc) if the problem is not fixed by the upgrades, you will chasing your tail trying to figure out what's going on plus chasing any potentially new issues created from your upgrades....
Identify the problem first. Try gutting the cats and seeing if the problem goes away. If it does, OK then, have at the upgrades. If not, well then, you just saved yourself a shit-ton of wasted time and headaches from all the other variables and trying to unravel the mess you could've created for yourself.
With so many variables thrown into the mix (new parts, new tune, etc) if the problem is not fixed by the upgrades, you will chasing your tail trying to figure out what's going on plus chasing any potentially new issues created from your upgrades....
Identify the problem first. Try gutting the cats and seeing if the problem goes away. If it does, OK then, have at the upgrades. If not, well then, you just saved yourself a shit-ton of wasted time and headaches from all the other variables and trying to unravel the mess you could've created for yourself.