Not sure that citrus is rabbit safe, don't think it is. Apple, willow, hawthorn, pear, are some rabbit safe woods. No pitted fruit like peach, plum, etc. If you can't get safe branches, the hay cubes may work well and you can get them at most pet stores or online. It's possible as he continues to grow, that the teeth problems will correct themselves.
http://www.medirabbit.com/EN/GI_diseases/Food/Branch/Branch_en.htm
With the URI, a good place to check for continued nasal discharge is on the inside of their front paws, as that is how they will usually wipe their nose. If it's crusty or matted at all, then likely the nose is still runny. Hopefully the abx clears it up, but sometimes it can take a month or more of the antibiotic, as URI's can be quite difficult to clear, and sometimes it can be difficult to find the right antibiotic. If he still has a runny nose after this course of abx and it is believed to be due to a URI and not some other sensitivity, you may want to ask the vet about having a culture and sensitivity test done on the bacteria. It can sometimes be inconclusive, but it also may help positively identify the exact bacterias involved and the best abx to fight it.
Another consideration with nasal discharge when it is clear and not thick and white or colored, is that sometimes an environment change such as being in a new home, can sometimes cause some nasal discharge, especially when a rabbit is coming from a cool environment into a warm home. Also other things that can cause clear discharge are sensitivities to household chemicals or smells, as well as dusty hay or bedding/litter, or a sensitivity to a particular hay or litter. Sometimes just switching to a different hay/litter can clear these type of things up, like if you use a soft paper litter, try a wood pelleted litter instead. Another cause of a damp nose can be a rabbit that is very hot and trying to cool off. Usually their ears will also be flared and they will be breathing faster and laying down a lot, in which case you need to take active steps to help them cool down.
http://www.medirabbit.com/EN/Respiratory/Bacterial/URI.htm