I tried that. I got these light wieght plastic things that fit over the registers and redirect the air. The problem is that it is stll under the drapes and when I open or close the drapes, it pushes the diverters away. The drapes come to the floor. I really don't mind moving them, if that's what's best for heating the room. I just want to make sure that it isn't a mistake, before I have them moved.

Here is what I think is going to play out best for you if you are going to be in the house long enough and will heat primarily with wood. Keep in mind that I am an amateur with absolutely no experience in duct systems. I decommissioned mine at the first opportunity and installed mini splits. I'll gladly accept all criticism from anyone that actually knows something. Berto, you've already said that you are going to have ducted AC, (I'd look at mini-split heat pumps, but that is me and I don't have the time to split wood.) It ought to be pretty simple to make a dual furnace system with a wood furnace first in series with the (second) propane or electric furnace. Your thermostat turns on the AHU blower (for me, ideally, a variable speed blower with a proportional thermostat). If the wood boiler is supplying sufficient heat the secondary furnace does not run. If the duct temp between the furnaces falls below a set temp (which might slide depending on outdoor temperature) the secondary furnace fires up. If the day comes that you tire of cutting and splitting wood, you pull out the cheap furnace and put in a mod con furnace. It is no biggie to toss that first furnace because it was inexpensive to start with. The duct system has to be designed to support both heat sources and cooling. The furnace that you choose will have to be just good enough to run a cooling system well which might be more costly than the least expensive that you might use for (back up) heating alone. Keep in mind that a (complicated) super efficient furnace or boiler is not going to be a good investment in a well-insulated and sealed house that is primarily heated with wood. The ROI time will look like infinity.

Yes you have been heating the basement, and yes you can reattach the flex duct to the elbow. Use foil tape, not duck tape. (I call it duck tape because its not for ductwork). Get the flex duct inside the insulation around the elbow and tape it down. If it doesnt fit then you will need an adapter, if the elbow and flex duct are the same size it will fit. Kind of looks like they tried taping the outside vapor barrier which ripped.

From what you described removing it sounds fine. But I'd recommend you bring a pro in to inspect it and patch it up, especially if you need to patch an exterior wall. You'll want it done correctly so no air or critters make their way in.