Mine was the same way,I loosened the nut and turned the threaded rod to adjusted the pedal. You can see the pedal lifting. You will also have to adjust the brake light switch

 

Have you tried bleeding your rear brake caliper?

 

You can adjust free play/pedal position by removing the side plate and adjusting. It's been a while since I did this so I don't remember the exact procedure I used but I seem to recall it was obvious and strait forward once I removed the plate and saw how it was connected.

 

As PDSF mentioned, he already adjusted pedal height but would like less pedal travel.

 

Yeah, I had it apart but it wasn't clear how to adjust the travel. I'm sure I just missed something obvious, hence the post The bike is brand new so hopefully the brakes don't need bleeding, although you never know about the setup guys.

 

I've noticed the same thing, more travel than I would like, and I didn't see a way to adjust that. Something I did that helped just alittle was fill the reservoir as full as possible without it sqeezing out when you put the lid on. What this does is reduce the amount of air in the top that will compress when you apply the brake. It will hardly make a difference, if any, but it's something to try.

 

This should make zero difference in brake pedal feel.

Look at the parts picture. If you can't get what you want, have it done by a pro, its brakes you are messing with. Be sure the light switch is adjusted properly too. Its one of the first things I do with all my bikes. It has to fit ME.

David

 

Copied from the manual

Brake Pedal Position Adjustment
NOTE
○Usually it is not necessary to adjust the pedal position,
but always adjust it when the push rod locknut has been
loosened.
• Remove:
Right Rear Frame Cover (see Rear Frame Cover Removal
in the Frame chapter)
Right Front Footpeg Stay (see Brake Pedal Removal)
• Loosen the locknut [A] and turn the push rod with the hex
head to achieve the correct pedal position.
If the length [C] shown is 70 ±1 mm (2.76 ±0.04 in.), the
pedal position will be within the standard range.
• Tighten:
Torque - Rear Master Cylinder Push Rod Locknut: 18 N·m
(1.8 kgf·m, 13 ft·lb)
• Install the right front footpeg stay (see Brake Pedal Installation).
Torque - Footpeg Stay Bolts: 34 N·m (3.5 kgf·m, 25 ft·lb)
• Check the brake light switch operation (see Brake Light
Switch Operation Inspection in the Periodic Maintenance
chapter).

 

Speedy at Moto Werk offers an adjustable brake lever nut that might solve the problem you've mentioned.

http://www.shop.motowerk.com/Adjustable-Brake-Lever-Nut-KVENZ-AD-BR-NT.htm

For what it's worth.

 

All that allows is more adjustment as far as positioning the brake pedal.
The only way to adjust the throw of the pedal is to modify the length of the lever or the size of the master cylinder. You have to move more fluid for a given throw.