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I am a brand new owner of a 2000 f250 SD 7.3 PSD. I bought it about a month ago with 43,000 miles and I always drove it with the windows down. Since the weather is getting warm now, I have rolled down the passenger window while driving. When I did that for the first time I noticed a loud clapping noise coming from my exhaust when I accelerate hard. I have never heard that before from deisels. It is very loud, to the point that my friend can hear it several blocks away.
I'm not sure if this is the problem but check to see if your exhaust pipe is rubbing against the frame or the body. I have a 4" exhaust on my truck and I recently added a 5" inch stainless tip and I heard this loud weird noise after I installed it and come to find out it was the pipe rubbing against the body. Again this may not be the cause of your problem but it maybe a start. Just my .02
i don't know much about this truck or much about what a stock exhaust looks like. i am very new to the deisel world. so, i don't think the muffler has been removed. i bought it from an elderly farmer in eastern kansas. in regards to it rubbing aganist the frame; the noise it is making just doesn't seem like an exhaust rubbing against the frame. it sounds like a deep slapping roar. but i will get under there tomorrow and check to see if anything looks like it is rubbing.
thanks