Whatever it is it's gone after warm up. It's not all too mechanical either, and I just finished the entire timing component replacement so it's not that. Plus, it isn't coming from the front of the motor.

Hi Sniperx
my 85 RT sounded like that, and went smooth after warmup. I was told it was the output shaft rivets being worn. I chose to ignore it when I saw the work involved fixing it. There are a few good write ups about how to inspect them without completely taking off the right hand cover (and radiator hose).
Do a forum search on output shaft rivets.
Could be other problems as well, that's the one I know of. The experts will be along shortly to put you straight.
I have heard a few K s over here with the same symptoms.
Good luck
RT

Rt is right about the rivets rattling on some bikes, also and equally as possible is the spring on the drive gear from crank to output or balance shaft, call it what you want.
A balance of the throttle bodies will eliminate everything else. Wear in the spring on the backlash of the crank/balancer gear can sound like a rattle in there at the back of the motor. Rivets or spring are possible as everything warms up and settles into the position it likes the noise is gone, so early days, when it rattles when warm it will start to be annoying and warrant investigation.
Do a search for those items and you will come up to speed on them. 
Might be odd but the odd bike has had the clutch arm touch the zorst and clank causing the owners concern till identified and reset.

One other thing, if you have replaced/upgraded to the K1100 front end/floating rotors: mine rattle a little bit upon starting and during warm up.  But after warm up, things run smoothly and this doesn't happen. Probably the other explanations above are more plausible (and certainly are if you don't have floating rotors), but thought I'd mention it, just in case.  Took me a few minutes of lying on the ground under the running bike and listening to figure it out.