One of my favorite sayings is "Everything is difficult until it is easy." Some things take a lifetime to master. Regardless, kudos for putting forth the effort and succeeding.
I'm going be cautious about sharing too many of my thoughts regarding cooling, as it tends to be a controversial topic around these parts.
Bassett has this
http://www.bassettracing.com/faq1.htm to say about water lines.
In another thread, Timm posted:
The Bassett "T" is a small on/off regulator, it keeps water out of the exhaust below about 1500-1800 RPM, that's normal. In the -8 fitting on the "spider" (that's the small lines that screw in the headers themselves) there is a double male that connects it to the feed hose. That fitting, if correct, has a divider in the center, and that divider has a hole from .080" to .120" diameter to regulate the amount of flow into the "spider". It sounds as if you either don't have that proper fitting, or the hole is too large. These exist because there is a great deal of difference in the pump pressure and block pressure found in jet boats. What was fine with your near stock engine will be too large when the new engine spins the pump faster and to a higher pressure.
Always replace the calibrated spring and ball in the beginning of every season too, they rust and corrode. Timinator
The setup in my boat utilized a mechanical fuel injection jet to restrict flow to the spiders in this same manner.
If you are using the typical -3 to 1/8NPT JIC fittings
http://www.mcmaster.com/#50635k371/=xram4m, they have a .125 minimum inside diameter (ID), which does not provide much, if any, restriction after the .13 ID tube the spyders are constructed from.
I think too much flow at too low a pressure will cause water to stream out of nozzles rather than atomizing to cool the hot exhaust gases. The high volume of water streaming does not evaporate but pools in the bottom of the header primary tubes where the exhaust pressure blows it out of the weap holes.
There is much written about this topic here. Before I go telling you you to redesign your system, I suggest you read up on the topic and then evaluate exactly what you have. Then you can make an educated decision on where to go from there. Remember that there is always help here.
Good luck,
Joe