I hear a heavy a metallic thunk when I increase from mild braking action to medium braking action with the clutch in.

I've noticed it a couple times in the recent weeks and I'm getting a little concerned.

Where should I start looking? The bike is still stock.

 

Maybe the caliper is loose giving you slop when you brake hard. Try that first

 

Assuming this happens with the front brake, cause that's the one you use the most.
Try getting on the bike and standing it up with the engine off.
Hold the brake lever on and try rocking the bike back and forth.

If you can make it clunk that way it might be easier to tell where its coming from.
Odds are that its just a loose brake caliper or steering head bearing.

If you can't duplicate it that way, just go over every bolt in the front end, including the rotor mounting bolts to make sure nothing is coming loose on you.

 

I have the same thing happen when I use the rear break heavily....

 

I have the same thing happen when I use the rear break heavily....I have a 2012 FXS

 

Wheel bearing?

 

Neck Bearings?