We have three hot water systems and none of them have both pumps running full time. Your system is setup wrong.
The circulation pump from the stove (outside circuit) should run anytime the water is above your set temperature. IRC ours are set at 180 degrees for this. This is the outside loop. Then the house or inside circuit should be setup to be controlled by a thermostat in the living area. This should run that pump ONLY when the house needs heat.
Your current system is trying to regulate the water temperature for the entire system by controlling the fire/draft. That systems is doomed to fail because of the different demands on the draft. You have to have a minimum draft just to maintain the fire. So in your case I would bet that your "new" outside stove is larger than your old inside one was. So even with a low fire it is generating more BTUs than you need for the house right now. So you need to stop putting the BTUs in the house. This is why you need to control the house pump separately.
With the outside circuit circulating the water it is unlikely to overheat the water. Also you can make the minimum draft lower. Most stoves are adjustable. If not make the opening smaller and see how it works. If it is a program running the blower every so often then your will need to see if you can change it to longer intervals.
Your "new" system needs to be controlled differently than your old one because your new system can generate more BTUs then your old one. Manually controlling the old system worked because it did not have much extra capacity. Your new system does so you need to have a better control then you had.
Mine work like this. The outside circulation pump runs whenever the water temperature is above 180 degrees. The forced draft runs when ever the water temperature is under 220 degrees. (mine are pressurized systems. If yours is not then your temperatures are just lower so you do not boil off the water) The house circuit only runs when the house thermostat demands heat. The draft fan does not run when the water is up to temperature. The draft fan housing has a small hole/slot in it to allow a minimum draft to keep some fire in the stove. It does not take much.
I would bet that your minimum draft is way too much. This can also be a program issue on the newer stoves. Mine just use a mechanical control. Some of the new stoves run the draft blower every so often just to keep the fire going. You need to run yours less.
I still think just controlling the house circuit with a thermostat would be all you need to do.
P.S. If your get your setup to really regulate the draft to a much low rate at "idle" then be careful when you open the door to add wood. If the stove is smoldering and you open the door an give it a big breath of oxygen you can get a big BOOM. On my first stove you could get the door open very fast and it would flash burn if you where not careful. The next one we had had a complex handle latch that took time to open. This way it would slowly fire up. The newer ones we have run the fan for a while before you can get the door open.
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