Firstly, i'm sorry to hear of you, your family's and your son's plight in this matter.
Secondly, I am not a medical expert, by any means, but I have an interest in many sciences, etc., including biology and related fields
in most cases I would tend to think that contact with most 'household' sources of bacteria (including things like dirty tissues) would not lead to infections of this nature, much less using a pillow that has come into contact with such, unless the source was particularly virile. I.E. The difference between a normal dirty tissue and a dirty tissue that was used by, say, a contagious flu sufferer.
From what you described, I personally do not think this sounds like an outer ear infection, strictly speaking. I would be more inclined to think it was a middle ear infection that may have penetrated further than the ear drum, how or where into I could not say. I'm not sure as to how a middle ear infection would be able to cause the ear canal to swell like you have described, however, I would propose that what has occurred is that an outer ear infection has possibly arisen from a nasal infection that has spread into the outer ear via the middle ear.
Your description of a yellow/green nasal discharge and fever would seem to indicate a nasal or middle ear infection and this would be my suspicion in locating a source of infection.
If the problem persists, my advice would be to push the point with the your family doctor and/or ent doctor. I'm in australia, so I can only speak from a relatively small realm of experience, however I would advocate finding a doctor that is willing to take more of an interest in this: a doctor that cannot explain a condition and then is not curious about it's occurrence does not sound like a doctor that is taking you seriously.
I also find that a number of doctors I have been to seem to think that if they cannot see anything wrong, then there is nothing wrong (and therefore the it's in the patient's head).
Regardless of whether you stay with your current doctors or find better ones, be sure to labour the point and push to get what you want. Do not stop until you are satisfied that nothing more can be done. Of course expense will be a factor, and here again I sympathise if this is not a meetable requirement, as I am currently a poor man myself undergoing expensive and continual ent consultation as well as university study.