I need to change my centre piece, I have one from a tf 3 litre but from my previous experience the cats are smaller on the 3 litre. Will I have any negative effects if I use a cat and centre piece of a 3 litre? Are they the same diameter and will the smaller cat affect anything? Such as fuel economy etc

Get them both on the ground together and compare them for length, diameter, bend angles and mounting point placements - it's the only way to be sure.
You should be able to get a new centre section quite cheaply, if you need one. I paid $210 for a TL wagon one (included installation) and $179 for a TJ one (did this one myself). The TJ one was a Redback, I also needed a muffler - parts shop got me a Walker for $179, mated up ok to the Redback centre section.

The early 3.0l models had the smaller cats so your cat will be the smaller one on the tf. If u got the whole section from the cat back it'll bolt up no dramas. Won't affect anything.