Hi Mia. Does your bunny have a space of his own that he can retreat to/hide if he wants to be on his own? My rabbits were all free-roaming, except when I first brought them home - I figured being in a large open area in a new locale and with smells they weren't familiar with might overwhelm...
My buns used to get orangey-red pee and of course I freaked out at first, until I found out it was caused by pigment in food. Here's an article you might be interested in:
http://www.rabbit.org/journal/3-1/red-urine.html
I've beengoing through the same thing with my Spike these past few months where large tufts of fur have been falling off. I went to my local fabric store and bought yards of "berber fleece" which I fold into 4 layers and put in his litterbox instead of litter, and also anywhere he lays down on...