Came across this forum yesterday while researching a siphon problem we are having here. Just read through most of this thread on you problems. Hopefully I can help a fellow South Carolinian. Not sure I follow all that has been said, and I didn't read through in great detail, but I have been maintaining a siphon system here for 18 years. I designed it in consultation with some local engineers, oversaw the installation and have been maintaining it ever since. We have a 6.5-acre shared pond with about 12 feet of head. One 12" siphon and two 6" siphons, with 2" piping for the control vent (that induces and breaks the siphon) and the vent at the highest point to break the siphon as needed. I do the lion's share of the maintenance as the siphons are on my property.

As far as basic components, a picture is worth a thousand words, and I assume you have something like this.

https://www.tractorbynet.com/forums/attachments/pondsiphonimage-jpg.466506/

One thing I learned early on, is that the 45 degree ell at the outflow is essential to form a trap so air doesn't enter the pipe from the outfall and break the siphon. We didn't install that at first, and the siphon wouldn't kick in until the outflow to the creek was fully submerged by the rising water during a rainfall. When you speak of charging the pipes and a gush of water issuing forth but then stopping, and sometimes the siphons working but other times not (if I read correctly), that would be consistent with not having that ell at the outflow. Do you have one?

Also, rather than fashioning a cap for the outfall to use when filling the pipe with water, we installed ball valves. Work great, but they do get persnickety with time. Can't get one for the 12" pipe, and we have to clamp a (leaky) cap on the end whenever we need to charge it to get a siphon going to clear a plug over the intake. You mentioned a submerged valve, and that may be to valve off the intake piping below water level so you can fill the pipe without waiting for the pond level to rise enough to fill the run of siphon pipe through the dam. Just a guess, as I have pondered installing such a valve myself.

Beavers have been our biggest problem here, by far. They can plug our intakes beneath 12 feet of water in short order, and every time we manage to unplug them they move less water, as some detritus remains around the intake. We are at the point we are pondering mods to put our intakes in more shallow water just so we can clean them fully when necessary.

Anyway, hope there is some useful information for you here.

Steve