Do you have a line coming off the back of your head? I was struggling to understand your cooling but I realize now you have an aftermarket hull and your pissers are at the front of the tray.
There is a similar conversation going on in this thread.
http://x-h2o.com/index.php?threads/...actory-b-pipe-yamaha-701.196041/#post-2032644
If you have two lines coming off your head but only one from the pump, then the water pressure in your motor is likely too low allowing water to travel through too quickly to absorb the heat or too incompletely leaving hot spots.
It would be worth the effort to put in dual cooling. It's simple if you have to through hull tubes.
If you are happy with the way the ski performs, turning the pissers, as you have done, is sufficient. Your temps may be normal but your exposure might not be. I have a superjet with stock pisser locations, so much further away, and when I make hard turns and get sprayed that water sure burns, but never leaves a mark, more time to cool.