The reason why your wood furnace is over heating is simple
The reason why your wood furnace is over heating is simple, when the draft fan shuts off, the natural draft of your chimney is still pulling air through the fan unit. I have one on my Hotspot and the design is very poor. If you want automatic control, the unit would need to be heavily modified. I gave up on mine and don't use it at all. I would guess you could add a shut off valve, plus the air inlet in the firebox should be redirected to the base of the fire where combustion air is needed which would give better control and having the air come in below the fire instead of above, would also reduce the possibility of pushing smoke out into the house.
I bought my Hotspot wood furnace a few years ago and had nothing but trouble with it, overheating, smoke in the house, tons of soot and cresol in the chimney. But I was able to correct the problems by modifying the furnace. First off, the manufacture obviously doesn't know a thing about how to build a proper wood furnace and has made a number of stupid design mistakes. The good points are that the furnace is solidly built with thick steel plate and is inexpensive to buy. I had to block off the door vent, it was a real smoke leaker, and covered it with a plate with a small hole with a slide cover so I can check the fire without opening the door. I also put a wood stove magnetic thermometer on the front so I can monitor the size of the fire or heat output without opening the door and getting smoke in the house. I also ran a fresh air intake duct, 6 inch diameter, the same size as my chimney, right up to the furnace ash door. Switched to a double walled stove pipe and added a chimney extension for improved draft. Now the biggest problem with wood furnace is the fact that they over heat the house. This is why the better units are boilers, you build a fire and get the water really hot, but the circulating pump only runs when heat is needed. By having a large water capacity, the heat is stored until needed, while a hot air furnace has to dump it into the house to keep from overheating the firebox. So, with a furnace, you need to reduce the fire which makes a lot of soot and cresol. I found the simple solution is to add post combustion air and burn off the soot and cresol while keeping the fire small. I drilled a hole and ran an one and half inch size steel water pipe in through the front of the furnace to the back of the firebox and up the back to under the shelf and then forward to the edge of the shelf. The intake of the pipe has a drop leg running down to almost the floor to keep any smoke from backing out the pipe. Under natural draft with the ash door closed, air is drawn in through the pipe and is preheated by the fire, so when it comes out the end of the pipe it is hot and ignites the unburned gases. This allows you to close down the spin damper and burn a small fire cleanly without messing up your chimney or putting out a ton of black smoke. So now I build a small hot fire, let it get hot enough to turn on the furnace fan, then close the ash door and let the house temperature rise to 70 degrees and spin the damper close. If I haven't put too much wood in the furnace, it will raise the house temperature to 72 and then slowly run out of wood. The post combustion air eliminates most of the cresol and all of the soot, the smoke coming out of the chimney is much less and lighter colored, and soon is invisible as the burn progresses. The trick is also to know how much wood to add, you need to consider the outside temperature and how many degrees you want to raise the house temperature. That way once you are where you want to be, your fire will be down to coals and will not over heat the house. Learn to operate your furnace, for mine at 20 degrees outside, with a large fire and the spin damper closed, I stay even at about 70-72 degrees in the house. A lot depends on how well your house is insulated. The better insulated, the better it will hold the heat and the less you will need to burn and the less smoke you will make. Forget about all that nonsense about loading up the firebox and having long burns, for the Hotspot and probably all hot air furnaces, it is a myth. For even at minimum burn, the house will over heat unless it is very cold outside. The way to keep the house warm for long times is insulation, that will reduce your temperature loss per hour, allowing you to make a small hot fire, heat the house up to 72 and them let it cool down to 68. That is the real secret of operating a wood furnace, only put in as much wood as you need to bring the house up to temperature.
I have also added a catalytic combuster that greatly reduces emissions, but since it increases heat output, I only use it in colder winter weather when you want more heat. Since it will increase the efficiency of your wood furnace by 25 to 30 percent.
The best way of course of reducing emissions is to increase the insulation of your house, then you will need to burn a lot less wood and can go longer between burns, and will save you money even when you are not burning wood since it will also reduce your gas heating bill. Let's face the facts, most wood burning is only a supplemental heating activity, so insulation will probably save more money than the wood furnace will. I use mine full time, so the extra insulation reduces the amount of wood I have to cut, split, stack and burn, by 50 to 75% and allows the heat of a fire in the evening to last until morning (72-65).