You absolutely 100% need to throw out the soil it was planted in if you think you have root rot. The pathogens will still be in the soil. I'd also wash out the pot before replanting. To me, the roots look fine and I'd just replant them. Make sure you are using pumice or some other inorganic fast drying material mixed in with your potting soil. If it were me, I would go, 2/3 pumice, 1/3 potting soil and pot it in a small planter. They don't have much root volume right now so there is no way for the plant to take up significant amounts of water. Just water it sparingly - probably once a month is fine right now. Once the roots have developed you could do it more often but the idea is that you never want the soil to be moist for more than 48 hours after watering. Root rot develops when a plant is subjected to periods of prolonged soil moisture. Its far easier to kill a cactus by overwatering than underwatering - remember that the cactus will start to get thin if it's not getting enough water and its very easy to simply water it a bit more...

Phytophera is rarely found in container soil, unless it is common garden soil that has been watered by surface water (creeks, rivers, etc) or by flooding (real flooding, not flood irrigation. I see no reason Agrifos would not work, or certainly would cause now harm in containers. The possible downside would be salt build-up which could be subsequently cured by flushing.

Thanks for all of your help everyone. I think I've done everything I can/will do for now. It's in the sunniest window in the house. Its been fertilized, and I think it's in a planting medium that will do. It's not Al's gritty mix, which apparently is just this side of the mix used to grow the Garden of Eden, but it's organic and seems to drain quickly. The tree has produced a few flowers. I don't know if that's good or bad or portentous, but it did. So I'm just going to enjoy the sent, and hope it survives until March. On another note, we have some warm days in the forecast mid 60s. I want to put the trees on the porch, but the temp is supposed to drop again and I'd need to bring them back in. Is it good to move them in and outdoors frequently if I'm not "hardening them off." Will that cause some sort of shock and mess up the one orange tree that appears to be flourishing?

If you leave any rot in the stem, there is big probability of plant continue to rot. Flesh should be of uniform light green or creamy color. Did you try to search this site? - there are many threads with excellent photos here on the same subject.