I'm busy learning about radiant floor heating as I prep to build a house this spring... We're planning to just do the basement floor at present, and we'll heat upstairs with wood or pellet stove. We won't be able to close off the basement from the upstairs, so I'm planning to use a floor temp sensor or two in the basement, rather than traditional thermostats.
From what I've read, the only real issue I see with your setup is that you're running a zoned system where you shouldn't be... Your "solution" is how it should have been set up from the beginning, since you don't want to close doors. Zones generally either need to be really large, or more or less sealed to work well. Your problem may be compounded by thermostats that don't quite agree on the temperature, biasing the bedroom zone to run all the time because it thought the temp was a few degrees cooler...
Bottom line: I don't think a zone setup is going to work well if you're not going to close doors to separate the zones.
I think also you keep saying "plumber" when you mean HVAC guy?? A plumber is generally NOT a HVAC expert, but is good at ensuring poo flows downhill, and the hot is on the left, cold on the right... If you hired a Plumber to install your heating system, you may be at least partially responsible for your troubles...
I'm 43, and I usually find that when I have problems, it usually IS my fault...