If you were to pull the exhaust off and look inside at the junction shown in the picture, the right side exhaust is restricted by ~40%-50%. In the last three stock headers that I have had, all three were made the same way.

 

Like insulinboy said it's a 2-1-2 system. It does not bleed into the mufflers at the same temp at all rpm's. At low rpm's (low backpressure) most of the exhaust from both cylinders is fed into the left can (the junction under the back of the pan does this) and then once rpm's builds up the pressure evens out and both cans will get to relatively similar temps. The real way to see if either of the cylinders are running cool is to put your hand near the exhaust right where it exits they cylinders (the header). Both should be too hot to touch. My guess is the bike was idling for a bit before you tested the temps, or you you were cruising at low rpm's before you tested.

As a side note, this is why people often have a hard time making a custom 2-1 exhaust for this bike. Whatever fluid dynamic design Honda did on the pipes and aribox is hard to replicate and improve upon unless you really know what you're doing.

Edit: I'm not so sure that the front pipe is longer than the rear... I think if you were to uncoil the rear one it would be longer than you'd guess... but that's just me, I haven't actually measured it out. It certainly has better exposure for cooling.

 

I think both would be very close I length.

 

 

WHEW,

Thanks for relieving my fears. It is obvious after you guys pointed it out, Thanks for the information, and the patience.
Our season is quickly coming to an end, a quick 5 months until she'll see the 'hot' tar. I intend to get into the motor this winter/spring, install the Manual Cam Chain Tensioners, tear into the carbs (I was told when purchasing it had a stage 2 kit??? whatever that means), and play with the rear sprocket a bit.
I assume the compression numbers for each cylinder is in the manual?
Well, anyways...
THANK YOU!

 

You have unobtanium and the bike probably hits 140-145hp on that upgrade alone! How many speeding tickets do you have?

Yep, somewhere around 160 as I recall.

 

Perfect, thanks.

 

You'll be able to tell which kit is in there once you get in. FactoryPro and Dynojet are by far the most popular, and often coupled with a K&N filter to further induce tuning nightmares. The jets are labeled and members on here can identify which one you have pretty quickly based on alterations to the slides and springs. I'd suggest reading 8541Hawk's Carb Setup thread as a base if you haven't yet.