I agree about pump one it should be on a bypass loop or removed. bypass would be best. If you do decide to install in zone valve. They are normaly closed you should wire it to open when pump 2 runs. You should consider some check valves if you do not have any lot of the new gunfos pumps come with them all ready installed so check before you spend the cash. A zone valve will make sure that loop only gets water when you want it to even if you do nothing with pump one

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If you simply remove pump one - The remaining two pumps will not be in the best position - they will work and the over run on the large zone should subside but?

The zone circulators and flow checks should be located on the supply side of the zones to minimize heat migration. Since no expansion tank is shown, there is no way of knowing whether the circulators are attempting to “suck” rather than push flow through the zone circuits.

What about replacing pump 2 and 3 with valves adding a bypass with a valve and balancing the system so that both areas have the flow needed to be happy off of one thermostat? Sounds like you like you like the house cooler so use the office thermostat to control boiler and pump 1.

Of course with the less expensive manual valves it takes a bit of patiences to get the flow matched for the desired temperatures.

Just a thought. I was hoping it would not class me with the "Numb-nuts".

That is also a workable plan CJ

He wouldn't "Need" to add the bypass as you describe and if it was in it would need a variable flow compensating valve to make up flow when both zones called. And in that it requires purchase of two expensive zone valves because the flow will (unknown at this point) be more than the capacity of a common 3/4 residential zone valve.

So in this case (this time) zoning with pumps as a plumber might - vs zoning with valves as a heating guy might, makes more 'cents' and JA doesn't need to buy two expensive valves and a regulator or new variable speed pump. He still will need some check valves and maybe the pumps have them built in - maybe not - I have not looked at their specifications. But I am sure his plumber and infectious pal "Steve" (Think that is his real name?) will be help him out on that.

the wax motor style is not the best choice short life. look for an erie style with end switches. one per zone, one stat per zone. relay to turn your pump on.
stat calls, valve opens, end switch makes pump and boiler start.do it right and you will be happy. just my thoughts and everyone has one. if you would like me to draw it out i can. good luck, jeff

I had a similar problem to what you were having JA...and ended up putting a 110 gallon water tank in line where you have pump #1. So anytime the boiler was running, pump #1 would be operating and with valves in line also, I could reduce the flow through my boiler, properly setting the differential temperature across the boiler. The rest of the hot water loop then had to come off the tank, not the boiler and this solved my problem. I put in lots of extra valves so that helped in balancing. Am sure you figured this problem out by now....