Hey all! Since I didn't get any feedback other than from tamara (thanks!!), I followed her advice about leaf removal and re-potting.
After removing the leaves (I ended up removing the entire stem from the trunk, although I haven't been keeping a close eye to see if I have regrowth at the places I removed from) mid-November, I have had a couple more turn yellow that I removed. It's still getting new growth at the top that looks nice and healthy, but the older leaves are looking a little ragged (I left the yellow spotted leaves on, and the ones that were a little brown on the tips).
Even though it's winter, I decided I would re-pot today to make sure all possible mildew is gone (it was also getting loose in the pot from me pulling it out to check the mildew situation, and needed more soil).
I got rid of all of the old soil and a bunch of the root-ball. I then used a mixture of about 1:1:1 of pine bark (mostly fine), black lava rock (recommended pumice, but scoria is supposed to work just as well), and perlite (a little less of the perlite and a little more of the pine bark, because I was worried about it getting enough nutrients). I read about this elsewhere and the gardener's after-pictures were amazing, so I'm hoping it will work for me too!
I was going to mix some Osmocote in as well, but I forgot to bring it with me to work so I will add a pinch of it tomorrow. The advantages to this mixture is that it drains really well, but the lava rock and perlite help keep it moist longer (so don't have to water as often), and the bark provides nutrients as it breaks down over time. I'm a little worried that the lava rock I bought may be a little too coarse (medium-sized pieces instead of fine), but that was all that was available to me at the time.
Before putting the plastic pot with drainage holes back in the decorative pot (which doesn't have drainage holes), I put a bunch of river rock at the bottom to elevate the plastic pot from any water that runs through.
Hopefully this will rid me of the mildew problem, and encourage my plant's growth! It is now sitting a lot straighter in the pot (you can see in my old pictures that the trunk was at a severe angle) and I hope it is happy with it's new soil. There are a few new pictures I've taken after re-potting it:
http://picasaweb.google.com/amharper/PachiraMoneyTree?feat=directlink I will post more pictures at a later date to follow up about it's progress.
One thing I did notice while changing the soil is that two of the trunks are dead (I think they were dead when I bought it, because they never grew leaves). I'm reluctant to remove them because it will ruin the braided look, but I will consider removing them at a later time (I think the re-potting and removal of roots is enough stress for one day). If my plant looks like it is doing well I will also start removing the more ragged-looking leaves.