I installed my Borla S-Type Axlebacks about a year ago and love the sound. My only problem is after about 4 months I started getting a rattle at about 1000rpm (it goes away at lower and higher) that sounds like it's coming from the exhaust. Everything is tight still so I'm not sure. I was also thinking about doing the rest so I have a full aftermarket catback.
Installing an engineered cat-back exhaust would be the way to go. Pretty much all of them are 3" pipe, so will support a blower or turbo setup.
1. Is there something wrong with my S-type? I am thinking about taking it into a muffler shop here in Columbus to see if I missed anything that could cause this
Quite possibly, something is contacting the car. Check it when everything is totally warmed up- your exhaust system grows by as much as 3/4 inch when hot, so what looks OK cold can touch the car when expanded.
2. What is the best pipe setup for the Coyote motors? X-pipe, H-Pipe, true duals? I plan to eventually put a supercharger on it but it will be a while (budget and other things) - I'd just like to lay the best framework for it in advance.
Do NOT eliminate the crossover pipe! H pipes (what the car has now) will provide more of a bass rumble, while X pipes will have a higher-pitched, raspier sound. There will be no noticeable performance difference between the two. The car will sound horrible and lose a lot of performance without a crosssover. As I noted above, manufactured cat-back exhausts will support a blower. Even though it's cheaper, avoid having a muffler shop fabricate the pipes. It won't have the needed engineering behind it.
3. Will I need a new tune for this? I know for air intake I would but not sure for compression changes.
No, even a full cat-back exhaust will (should) not require a tune.