Ugh, no water flow is not a good thing.
For more info, consider the following thread:
http://www.moyermarine.com/forums/showthread.php?t=726
It sounds like you have a clog or a pump problem if there is no water at all at times.
The previous owner of my Atomic 4 had flow but high temperatures after longer periods of use, and he did an acid job on the water system. After that, it seems fine. He noted that the rpm of a healthy Atomic 4 fresh water system was around 5 gals (out through exhaust), and he had tested my engine by letting the exhaust fill a five gallon bucket in about a minute.
I have the Moyer manuals and some of the original manuals-- haven't seen online ones, other than the advice given at the Moyer Marine discussion boards linked above. I could check the manuals this evening to confirm the rpm rating.
Good luck!
Jim H