When I setup cooling, I test it on a trailer first. I have cold fusion pisser which are adjustable and they can be pretty helpful. If you're running the setup I mentioned, you may need to restrict the pisser near the stinger to get enough flow to your headpipe and flow control valve. It's easy to test your fcv by just taking it off the stinger, hold it over board and see when it opens and see how much it flows.
To determine how much flow to your headpipe, you pretty much measure that by how hot it and your chamber gets.. When setting up headpipe pressure, I like to have the top screw on my pipe opened more than a turn, just to rule out the possibility of the chamber sizzling due to the screw adjustment. If the headpipe gets really really hot and the chamber sizzles a lot with that top screw opened a bit, you need to restrict the stinger pisser some more. I like to get enough pressure to the headpipe to keep it nice and warm, but give it a decent amount of spray through the adjustment holes(the headpipe is water jacketed just like your cylinder).
The more pressure to your headpipe, the stronger the spray into adjustment passages to tune the pipe. Test it wot to see if the chamber is at a warm temp, then I like to close the top screw completely and open up the bottom screw to get my desired chamber temp(it totally depends on the pressure to your headpipe, but I'd open the bottom screw more than a half a turn and test it wot/high throttle for like 30 seconds and splash it with some water. If it sizzles a ton, open up the bottom screw. If it's nice and cool, turn it in.
Believe it or not, the screws can be very sensitive. I get mine so it's lightly sizzling on the trailer, but remember that it'll run cooler when you're ripping it like normal, since an aggressive intake grate and the forward movement will force more water pressure into the pump compared to on a trailer(that's my experience).
My pipe sizzled at 1/2 turn on the trailer, and when testing it on the water, it ran very cool. I ended up with it just cracked, probably around 1/4 turn and it lightly sizzles after extended high throttle/close to wot runs. No melting anything, and it absolutely rips off of the bottom to the mid range powerband.
Zack at php recommends tuning with bottom screw, all on with other people as well. When I was using the top screw, the powerband was crazy from mid to top, but with the bottom screw the bottom and midrange is pretty much perfect for setup wakes and jumping waves/surf.
In terms of engine temp-I haven't really need to adjust that much. Since I'm using adjustable pissers, my circuit coming right off to the head to a pisser is slightly restricted. But both my cylinders are pretty close to the same temp. They're pretty warm after a lot of hard riding, but I can hold my hand on the side of the cylinders for over 5 seconds without it becoming uncomfortable. The pisser coming off of my head is nice and warm, and the one coming off of the tee(the stinger circuit) is fairly hot. This is normal I believe, because this circuit runs through the exhaust, and the exhaust is fairly warm. I can put my hand in the stream, but it's not real comfortable. But both my cylinders run at the same safe temperature, so that's what matters. My water temperatures are around 70 degrees, and everything gets plenty warm.
I'm running a 701 61x/61x, 44mm carb, Ada head with 35 cc domes(180 psi), 9/15 hooker prop, worx 201 intake grate, stubby pump cone, etc. Tapped my pump for dual cooling and added a line so I can still use my bilge siphon.
There's my.02 for setting up cooling, and it works awesome for me.
Edit: T handle adjuster screws and a short open ended 3/8 wrench make the bottom screw A LOT easier to adjust.
A user by the name of Parrdaddy(sp?) sells them. Totally worth it. And keep your pipe screws lubed with antisieze, zep, wd40,grease,whatever you have laying around.. Siezed screws suck..