The stomach cramps and nausea sound more like your liver rather than your stomach (and liver will affect stomach anyway). Sounds like the detoxification (urine is a potent detoxifier!) is possibly overloading your liver. You can't just eat junk and expect urine to maintain your health! You need to eat a healthy Diet alongside UT so your urine will be healthy too! Eating less junk will help overall as it will mean less toxins in your body, cleaner urine and less toxins for the liver to deal with when you mobilise them through drinking it!
Aim for a diet that is more alkaline than acid, so if you eat lots of meat or proteins in general and other acid foods make sure you balance this out with tonnes of vegetables especially dark green veggies for the calcium, magnesium and potassium (juicing is great for this). If the quality of your urine is poor due to poor diet, drinking it can make you feel a bit odd (acidic). You can buy ph strips from your local pharmacy to test the acidity of your urine.
Also you need to open the routes of toxin elimination ie regular bowel movements so enough fibre in your diet, exercise till you sweat, skin brushing etc as this will take the strain of the liver in dealing with the mobilised toxins.
Hope that helps!