I wouldn't build an exhaust system until you figure out which engine is going to be the "Final Word".
An exhaust built to suit the 5.7 will need revisions to stuff in an LS.
Deleting the catalyst will violate Federal law.
+1 on this. I put 2 high flow cats on my 1990 6.0 swap. I'm getting older and don't really like the smell of exhaust that much.
You CAN do your system now, but just be aware like Schurkey said, it will need to be modified with your engine swap, so that would be a con. Also, depending on your area, most exhaust shops will not install a full system without cats if the vehicle originally came with them. They can get in big trouble for that.