I have about 800 miles on the bike so far and noticed that the left cylinder appears to be running hotter than the right one. The left exhaust pipe has a longer amount of discoloration as it exits the engine when compared to the right pipe.
Just wondering if anyone else has noticed this or thinks it is of any concern.

That's from excess fuel burning in the exhaust header. Does it glow red hot more on the left side when idling in the dark? Maybe your thottle body vaccum synchronization is off a bit...
My Muzzy headers have a slight gold color, even on both sides. I haven't checked my TB synch now at only 400 miles, but I know my left TB's vaccum set screw is open 3/4 turn (right screw closed).

I just checked my TB sync and they were spot on at idle and at 5K rpm. Hopefully it won't be a problem.

Mine has this very same condition. I phoned a trusted bike shop who didn't think it's necessarily a problem. I've got about 3000 miles on the bike now and will be bringing it in later this summer for a pre-warrantee expiration check-up. It runs so well I'm hoping this is just normal. I'm hoping some experts chime in on this.

http://mototuneusa.com/harley_power_!.htm

Pic 2
Now look at the Harley pipes...

The color difference means that one cylinder is possibly correct, but they can't both be right.

Either the Fuel / Air mixture is wrong, or the left pipe's cylinder is burning a lot of oil. I didn't notice the Harley smoking on the track, so it's probably the Fuel / Air ratio.

I would say it's possible your throttle bodies are not synchronized.

Brian_nbmc, don't you mean the right header pipe, as when sitting on it?

It seems to be common, with the stock header at least.
http://www.versys.co.uk/index.php?option=com_smf&Itemid=45&topic=1141.0
http://www.versys.co.uk/index.php?option=com_smf&Itemid=45&topic=3684.0
http://www.kawette.net/forum/viewtopic.php?t=1415&highlight=collecteur
http://www.kawette.net/forum/viewtopic.php?t=2286&highlight=echappement+bleu

Second pic shows it on Kawasaki factory press photo for Europe's ER-6 version.

Invader, No, mine is the left header pipe as you sit on the bike. It is the opposite header pipe you showed in your pictures that looks like it is running hotter. Mine isn't quite as bad as yours though yet, as I only have 1100 miles on it so far. I showed it to my dealer and he said he was going to contact Kawasaki about it. I will post their reply say as soon as they get back to me.

I just checked my TB sync and they were spot on at idle and at 5K rpm. Hopefully it won't be a problem.

How does one check the throttle body sync (assuming that is what TB sync means)?

I used a motorcycle mercury vacuum gauge connected to the two ports on the throttle body. They are a little difficult to get at, but it can be done.

Mine isn't quite as bad as yours though yet, as I only have 1100 miles on it so far.

That pic is of an ER6 from the french Kawette forum... My Muzzy 304 grade stainless steel header still has just a slight golden hue equally on both pipes.