old_squid,
The 1 inch outgoing pipe from the boiler has a combination temperature/pressure gauge. There are no gauges on the pex lines going to the individual zones. The boiler's controller indicates there is a 2 degree difference between the outgoing and return. I turned off zones 2 and 3. There was no noticeable improvement in zone 1.
In monitoring the boiler's controller during one heating cycle tonight, the boiler heated to 166 degrees, even though the set point is 180 degrees. The combination gauge on the outgoing pipe read about 135 degrees.
Are there 2 pumps? One for the piping that looks like it goes from the boiler, through the 1" piping and then right back to the boiler with your heating zones tapped off of it. The second pump being on the piping going to your zones? If you do have 2, then the boiler system is piped primary/secondary which is the way it should be. I'm guessing this is the way it is because you said there is only 2 degrees difference between in and out of the boiler and with the issues you're having heating the zones this shouldn't be the case UNLESS you have 2 pumps. Or, you have other issues.
The difference between what the boiler control says the outlet temp is and the gauge could be because of any number of reasons. I'd trust the boiler control.
The set point being 180 and it stopped at 166 could be because the boiler has what is called a reset control either connected to it or built into it. This type of control will lower the actual temperature according to the outdoor temperature. The warmer it is outside the cooler the water can be and still keep your home comfortable..... as long as everything else is working properly of course.
If you believe the zone valves are working (I seriously doubt all 3 failed, because you say 2 & 3 seem to be working, kind of) I'm leaning towards your problem is with the pump that circulates the water through the zones.
Your problem (from your description) seems to be one of slowed or no forced flow of water through the zones. If this just happened all of a sudden I'd suspect the pump. If it's slowly become a problem than that can be a lot of other problems.
Flow through the system can be roughly proven by taking temperature measurements along the zones. Easiest way to do this is with an infrared temperature gun. They're fairly inexpensive and can be bought at most big box stores. They come in real handy for a lot of things around the house once you get used to using it. Just remember, if you're trying to measure the temperature of a copper pipe you need to put some black tape on it first. The surface of the copper pipe does not read accurately.
Start at the point where the heated water leaves the boiler area and heads towards the first baseboard zone and take a reading, writing it down. This should be your hottest reading. Tracing the piping as it goes in and out of each section of baseboard take readings on both ends writing the readings down each time until you get back to the boiler piping. Make a line drawing and put the temperature readings and arrows showing the flow along the line. The drawing doesn't need to be accurate, just a rough representation for a reference.
From the time the water leaves the boiler until it comes back the difference in temperature shouldn't (normally) be more than 20 degrees. This also means that if there are say 5 baseboard units on each zone, each should not drop more than 4 degrees. Large drops in temperature across zones means your not moving enough water through them fast enough.
Heat energy in a hot water heating system is moved from the boiler to the home and back to the boiler by the water. X amount of heat moved from point A to point B "basically" takes two things to happen in a hot water system. Temperature difference and flow. If you have the hot water leaving the boiler but, the returning water has cooled off more than 20 degrees you've not delivered as much energy as the boiler is potentially capable of producing. The closer the temperatures are between the supply and return the more energy delivered/moved (assuming that the water is flowing correctly). With a lack of proper flow you will also see the first baseboards of a zone working fine, but the last one not producing any or little heat. No energy delivered via temperature difference and flow = no energy/heat delivered to the room.
And that is your basic lesson in Hydronics 101, without the math. Good hunting!