Here are some close up pictures of the roots of this tree in question. Any ideas on what I should do to save this tree? Should I trim all the roots and replant it? I really appreciate any help in this matter. Tim.

There might be some of the smaller roots that might contain some rot, but from what I can see, the root structure does not look that bad at all. I really dont see that much of a problem. - Millet (1028-)

The root system doesn't seem to have totally collapsed. It looks like the root system of an old or field grown tree ? Has it gone backwards since you potted the first time ? Is it weak and slipping, ie if you tug at a peice, does the outer part slip, a bit like stripping the insulation from elect. wire ? If not, its probably not far gone at all. I would remove the dead blackened bits to lessen the chance of spreading infection when you re- pot. Take care when doing this, maybe use alcohol or flame to sterilize snips between cuts. If you are going to re- pot, I would use fresh mix, and place the roots in the upper 1/3 part of the new pot, rather than let them get into the lower part straight away.
Make sure when you pot up, that the mix is wetting up properly, and perhaps flush a bit to remove excess fertilizer/ salt. A lot of root problems start here, and allow infection to take hold.