My questions a

1. Shouldn't Taffy and Spunky have gotten over their "colds" by now.
It's been over 2 weeks. Any ideas?
I didn't see where they were on any medications for the colds. I would
highly recommend you get to the vet sooner and get them on something for it.

2. If not mites, why is Taffy's ear getting scabs/dead skin? Can
anything be done about this?
Its probably yeast. most vets recommend an antifungal med like tresiderm.
The other issue might be that since their eyes are watering so much, its
"backing up" into their ears, since all that is connected. I have a cat
with blocked tear ducts and his eyes and one ear is always covered in black
debris.

3. I don't think Spunky's "pancake stool" is normal, but she doesn't
seem to be in pain, is using the litterbox and is no longer vomiting.
I called the shelter where I got her from and was told that she used
to eat a variety of donated food and never had a problem. Is there
anything else I can do for her?

Take another stool sample into the vet. Very good chance they missed
something the first time. Feed her some yogurt and canned pumpkin. both
with help with soft stools.