David,
So the first question I would ask right now is where is the pond level in this moment? If it is overflowing the spillway ... then something is definitely wrong with the siphon. If it is overflowing the spillway and the water coming out the exit end of the siphon is sluggish, then I think the first place to look would be the inlet of the siphon as you suggested.
You may not need to do anything other than that to correct the situation. I would just mention that a 2" suction break seems a little large for a 6 " siphon. I would rather expect to see 1" ... possible 1.5". It does however depend on the head from apex to exit how much you need to restrict the suction break. I also expect the break to be at or near the apex of siphon (rather than under water). If your pond is flowing over the emergency spillway, the siphon should be roaring and if it is not ... there is either an obstruction or too much air breaking the suction. If your pond level is lower, you may not be able to charge the siphon sufficiently and will need more water flowing into the pond to get it to work. If the pond level is consistent with the apex of the siphon, then your siphon is just working to handle over-flow and a suitable suction will not develop because the flow is too low.
Rather than wait for rain, if you have a fair amount of flow that could fill the pond in a few days AND if there is no rain expected in the watershed for the same time period, you could block the exit of the siphon by installing a full opening valve to allow the pond to fill completely. When you open the valve, the siphon should go right to working. Personally, if I were to add a valve for a test like that I would take off after the suction was broken and my test complete. Anyways, once you have the siphon charged it is just a matter of fine tuning the suction break to shut off at the desired freeboard. The more restrictive the suction break (smaller diameter is more restrictive) the lower the level your pond will go before the suction of the siphon is broken. I really don't like a valve on a suction break (You never know who may come along and close it or what not). But if you could put a collar on it, you could test different sized reducers in it to see which stops the suction at the most desired freeboard.
One last thing, there is a limit to how much water can pass through a siphon. It is possible it was much too small for those heavy rain events. IOWs the siphon may have been passing all it was physically capable of and the flow into the pond just vastly exceeded the siphon's design. You many need to shore up your emergency spillway. There are concrete pyramid shaped thingies (sorry don't know what the actual name of those things are) that can be deployed. Not sure but they may have a spike that is driven in. I've seen them on spillways and even the dams of small lake-like ponds. Anyways the look like a pyramid with the top cut off and they are arranged in rows and work to deter erosion.
