#1 So use a good Probiotic after the fast. I'd use something like total immune Booster to help re-grow the good bacteria OR live lacto-fermented foods like Kefir, sauerkraut, kimshi (From Rejuvination Products, I found it in Whole Foods grociery store).
#2 The great thing about UT is that your body is getting most of the nutrients it needs from your Urine. During the UT fast you are supposed to drink all your urine and another 8 or so glasses of water too. Doing the fast using Urine will not leave a person hungry or deprived, your body is getting what it needs. Alot less suffering than a regular fast or so I have read.
A great E-Book is "Shivambu Gita" by Dr. G. K. Thakkar. Page 51 tells what is in Urine. He also mentions the body relying on just the urine during a fast. I highly recommend this book...
So good luck on your journey. Tonights got me back thinking, "Why did I stop drinking my Urine?"