No, the exhaust is not the problem. Did it do this before the pc, or was that on it when you bought it? I'de say put the fuel map back to stock, but if you've disconnected it, it should reset to factory settings, you could disconnect the battery just to be sure. Is the "noise" still there? I hate to say, but a noise from the top end and glowing pipes is NOT GOOD! A plugged injector is not impossible, but very unlikely with low miles.
Again, the exhaust isn't the problem, you can run a completely stock bike with full exhaust and have no problems at all. The pc will just give u a better fuel map to make the bike run smoother throughout the rpm range.
Your pc has the pushbuttons to lean or richen it, correct? I'm not familiar enough with that model to know if you could actually lean it out enough to cause damage. I guess that's possible, but I wouldn't want to say for sure.
I don't wanna jump to conclusions, but I hope someone didn't screw it up and pass it along to you. If you can give a few more details, like, did u adjust anything before u noticed the problem? How long did it take u to do 200 miles? For example, did it take u a month, and then the problem popped up? Or did u ride all 200 in a day or so, and it happened? Or was it something u wouldn't have noticed if ur buddy didn't point it out, so the timeframe didn't matter.
I've got a couple suspisions, but there are a few folks on here that will be able to tell u exactly what's going on. This post just hasn't caught the right eye yet.