Some people run a bypass from the front to the rear to equalize water temps across the cylinder head and prevent hot spots.
I've always just plugged them and never had any problems. But then again all those exta fittings and hoses all over the top of the engine looks pretty cool.
Here 's alink to a simialr thread about the same question on yellowbullet
http://www.yellowbullet.com/forum/sh...d.php?p=288725
Hope this helps.
Goodluck, Charles