Mark, with all due respect, your issue may very well boil down to just draft. You stated that the stove seemed to burn stronger in the basement, but when moved upstairs it is now anemic. Considering you just reduced chimney height quite a bit, that could play a role. Especially if this was from the onset. Also, I hope you are not sharing that flue with another appliance. But if you are, and that appliance has a baro, that would explain a lot. For sure you will know something when you get the mano hooked back up.