i am not an expert in any way, so maybe wait for some others to chime in:
if you suspect an exhaust leak(at the header), i would imagine if you unplugged one cylinder at a time while the car was running, the noise would go away when you unplugged the cylinder associated with the leak. if you check each one and the noise never goes away, it probably isnt an exhaust leak.
however, if there are leaks at multiple spots, killing one cylinder at a time wont remove all the noise, just decrease it, so you would have to pay attention to that.
now, again, im no expert, but this makes sense to me from a logic standpoint. exhaust leak noise is created by exhaust pressure. if you remove the exhaust pressure, you remove the noise. if you remove the pressure and still have noise, then the pressure isnt the source of the noise.
once you eliminate the chance its a header leak, you can move on to other potential problems, which is what you initially asked about, but it appears you arent 100% sure its not a header leak?
if this is totally wrong, somebody yell at me