With a 90,000 btu Pocono you will see about 72,000 BTU's when at 99%. You say that you have a 12" duct top, so that means that your loosing all of the heat from the sides of the stove. If you want all the heat upstairs and very little in the basement then you should have a hot air jacket on the stove. We sell our stoves as supplement heat, not furnaces. I think if I were you I would inclose the stove with a jacket, take off the 2-265 cfm fans and put a 12" duct fan inline in your run. I would hook the duct fan up to the coal trol and let it do its work. I think you will see a big difference in the heat going upstairs. If you have a buddy that's a tin knocker play with the jacket idea. If not, then we sell them.
If you don't want to invest in a jacket then I would suggest that you install a duct fan in your 12" run, but if you do, take off the convection fans that come with the unit.