Hey guys, i have a 2003 R6 and I have put about 15 000 miles on it to date, so I know what she is supposed to sound like. I have been keeping up with maintenance very well. As the title suggests, it has recently started making a very loud knocking/rattling noise coming from the engine. If anyone has heard this before and knows what the problem is or most likely could be from similar experience, PLEASE let me know. My R6 is my daily driver, so I would like to fix it before something major breaks.
I have attached a zipped audio file so you guys can hear what it actually sounds like. Sorry that it is only 4 seconds long, but thats all the space they allow for.

Any help will be greatly appreciated.
In case it would help, here is a list of things that has recently been replaced/changed - new timing chain about 400 miles ago, new clutch boss and basket also 400 miles ago, valves checked 1000 miles ago and no adjustment needed, oil change 1000 miles ago, throttle position sensor cleaned 300 miles ago, spark plugs changed 300 miles ago, coils resistance checked 300 miles ago.
As far as modifications it has - performance air and oil filter, hindle exhaust, power commander, 05 throttle bodies and air box, 520 chain and sprocket conversion.