Wood Furnace Overheating

You can use these type furnaces as a stand alone.
Necking down the duct work restricts your air flow and keeps the firebox hotter. Change your duct so it's 8" all the way to the register and it should keep the furnace cooler.
It sounds like there may be other problems but I wood start with the duct work.

I basically went with the 4" ductwork because of a fairly low ceiling in the basement. I also had to go with stand alone option because my other heat is electric and doesn't
have the plenum setup of conventional furnaces. If I go with the 8" ductwork to the registers, will I have a problem if the registers are in contact with the flooring and carpet? I was told somewhere that heat might not catch wood on fire right away, but over time it degrades the wood to the point of possibly catching on fire. Is this correct?

You need to provide clearance to combustibles because it's possible for unusually high temperatures. You can transition the 8" round to 4'X10" rectangular.

I finally got 8" ductwork going to the registers. It definitely dissipates a lot of the heat into the basement area, but still has more than adequate heat coming up out of the registers. I can now run the furnace at higher temps to make sure I'm not creating a creosote problem. I couldn't do this before because ductwork was getting very hot.
I have a thermometer on the face of the furnace, will this give me an accurate burning temp? Thanks for all the help.

yep good info to have

it should help you develop a good base line on where your temps are best. Its just one more tool to help run it better.

I used to keep my furnace in the 400 degree range in the front above the loading door. If you want to know how its burning, watch your chimney. I could push my temps higher, but I had a lot more air going through the furnace.