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I've got a 99 5.4 and true duals and i have noticed a torque loss and was wanting to regain some of that torque. i want a nice deep tone that has a little rumble to it. Any advice i'm thinking Flowmaster Super 40 DI/DO, but i'm not sure i could go with a Magnaflow. If i do teh flowmaster is DI/DO going to regain torque or do i need to go SI/DO??
The Flowmaster 40 series, as widespread as it is, is a good muffler. If you want a good loud rumble, that's the way to go. For just a rumble, run the pipes after the muffler out the back of the truck. For a loud rumble, dump it right after the muffler.
I have heard that simply adding a X-Pipe to a true dual system will really help with low end power and torque, I heard this from a guy on the forum. He has straights with stock cats, true duals, and a x pipe. He said he once had true duals with no linkage inbetween, and when he added the x pipe it was a huge difference, really helped the scavenging of the exhaust. I personally have a 4.6L with high flow cats, 2.5" true dual straights(no linkage whatsoever), angled out the back with 5X22" SS tips, I did notice a big drop in low end, but gained a lot at around 2000 and up. Just a lil info I thought might be somewhat useful.
The main reason you noticed the loss was because you went with 2.5" pipes, if you add an X then yes it will help. But you wouldn't have noticed it as much if at all if you had gone with 2.25", tune the exhaust and it makes a big difference as well.