uh oh cam timing

I own a 93 cbr 900rr and had to replace the head because the original had stripped sparkplug threads.  Having replaced the head and paying attention to the instructions in my factory owners manual, I fired up the engine but it is not sounding right at all.  I quickly shut it off.  I am now going to have to check the position of the cam postion in relation to the crank being in top dead center.  My question is am I missing any piece of the puzzel?  the manual says that the cam sprockets intake and exhaust marks supposed to be parallel to the head.  
Thanks For your advice.