My bottom line would be that you want to do anything you have to in order to get the standing water out of there. That may very well require some work to redesign the outside drainage lines. I'd look into an outside drainage system that fed into a nice deep rock filled pit that allowed excess water to disperse into the ground away from your house foundation. You may also want to equip that outside pit (also known as deep french drain) with a sump pump to take care of extreme heavy rain or high water table incidents. After the drain situation is corrected I would look strongly at correcting the landscaping and roof runoff gutters to you minimize the amount of water that the drain pit is asked to handle.
All that work can be done outside without tearing up your floor in the den. Hopefully the area under the floor would then stay dry like it should.
As far as heating....trying to use a soil and concrete "tunnel to bring heat into a room it terribly inefficient. I would find out how you can disable that part of your existing heating system. Then have a suitable sized direct vent heater installed in the room for in room heating. A direct vent heater sits on the floor by the wall and has a concentric pipe system goes out through the wall. The heater draws combustion air in through the outer cool pipe and exhausts through the inner hot pipe. I've installed one of these in a basement room that was more than half under ground and had good luck with it. Obviously you have to route electricity and a gas line over to the heater if you have gas type heating fuel (either natural gas or propane).
An advantage of the separate heating zone created like this is that you can easily regulate the temperature to suit that specific room or just shut it off it the room is not in use.
Obviously, the soil needs to be graded away from the house (in the back yard). If that means you need a retaining wall, then you need a retaining wall.
Regarding the swale, improved drainage sounds helpful. The real question is, why isn't water shedding (what is the real issue)? I've had swale issues, and the problem in those cases, was not with my swale, but the neighbors'... so water backed up in my yard. In such a circumstance, you can talk to the neighbors about the issue, ask them to fix it, offer to help, and/or sue them for damages.
But if the neighbors aren't to be blamed, then another alternative to keep the grass cut very short (grass slows drainage). Or you could check into a trench drain (concrete ditch). This is just another option that I didn't see mentioned, although it may not be your best option. As Tester101 pointed out, being there to see the issue is probably necessary.
Regarding power outages, gasoline or propane generators are the most reliable answer. A moderate generator should be enough for a sump pump, the fridge, and should keep the toilet flushing too. As you know, the drawback with a battery bank is that once it discharges, then you don't have a simple solution, like getting more gas.
Edit- Here's a possible way to use a retaining wall to increase the grade away from the house.
Best Answer
I emptied the water from this pit and after a day or so it started to smell like sewage in my basement. That's when I realized that this pit works the same way as a toilet. The water at the bottom block the fumes from the sewer. The oil-like substance at the bottom of the pit is some kind of sealant put there to prevent the water from draining into the ground below. I dumped some water down the pit and voila, problem solved.