Can i put magnaflow mufflers on a JBA shorty header / h pipe setup on my 1968 mustang coupe? (289)?
Yes. Keep the pipes small. That engine stock will make more power and torque with 2 inch pipes than with anything bigger. You don't have the Cubes/CFM movement through the pipe and engine to make the pipe scavenge the intake. If you want to gain about 35HP and 40 lbs of torque, put a single 2 -1/4 exhaust on there with a dual outlet muffler(for the dual look.) You'll have enough exhaust system to handle up to about 275 HP. Singles will ALWAYS make more torque and HP on a naturally aspirated engine, up to 7,000 RPM. Done right, you'll see bigger power and more gas mileage, too. It's a win-win.
Everyone thinks it's about breathing. It's actually about scavenge. If you build enough scavenge in the pipe, you'll scavenge the intake harder during the overlap phase.