I will make some observations just from looking at the pictures. I don't have headphones (and I'm at school) so I cant listen to the audio right now but I can later.
Try and get a microphone stand. I understand you may be trying not to buy anything else but I think even that could yield better sonic results. Maybe on japanese craigslist they could be had cheap? Or in a store? I dont know. I see your microphones are resting atop shoeboxes. You could try to cut a hole (circle) into the shoebox that your microphone can sit in. The ports are covered on the bottom side (laying on the shoebox). This won't be good for cardioid microphones (or for others but we're talking about ports but with cardioids, it subtracts the directionality). The microphone will be able to "hear" the tone of that shoebox I think. With the vibrations that the guitar is putting through the inside and reflecting on the outside. Another option is to hang the microphone from something and direct it to your guitar. Well I looked again at the picture and you have it hanging off of the shoebox, which is a better idea than just resting it atop it. You've seen shockmounts before.. thats why they make them, to get rid of the vibrations and sounds going through the mic stand .. to isolate the microphone from the floor too.
The room doesn't look that bad sounding but I guess that doesn't really make a good judgment. I see the pillows resting behind the microphones on the chair. You may have read this before but that is probably making the perceived sound worse. These pillows, while they are lessening reflection, they are detracting a lot of the higher frequencies in the sound. This is taking away from the perceived crisp, bright, and clear qualities that many people often would look for in an
acoustic guitar recording. Also, it seems like you don't want room reflections.. but when you're miking the guitars up close, you really won't get too much room sound. I'm not saying the room won't be on the recording but with close miking, the closer you get, the less you'll get of the room. I think for experiments sake, you should try putting the microphones hanging off of the edge of the computer desk. You should be able to hear a whole different "room" once you put them on the desk.
From my experience, when I rest a microphone on something other than a mic stand, I do actually lose a feeling of openness. See if hanging it from the ceiling with a piece of tape in the center of the room dramatically changes the sound. A lot of people like the sound of early reflections because it gives a little space to the recording. Try backing up from the microphone, try getting closer to it. Try hanging one microphone over your shoulder by your ear and the other on the shoebox.
With your set up, you may even get some phase cancellation. You could put the microphones in XY configuration and see if that makes a difference. I dont know many things about room design or really sound for that matter but I strongly believe that with a bit of experimentation, you can reap nice improvements in your sound.
I'm anxious to hear the recordings. Hopefully I can't hear the cardboard and pillows too much!
Good luck Monkey Allen.