The liver does not feel pain. When I got hepatitis from too much drug use and nearly killed myself, I felt no significant pain prior to waking up yellow and unable to move.
Sometimes an inflammed liver can put presure on other organs and created a dull ache in the right side of the rib cage. Also, a distended, gassy feeling is common if the liver is stressed and swollen. Don't ignore these warning signs.
Pain in the lower back is generally muscular, but not always. Your body tries to tell you when things are just wrong. Pay attention to it.
That being said, we must make some allowances for the fact that we are cycling. There is an intrinsic stress to the body that is to be expected, and a certain amount of unhealthiness is involved in this practice of steroid cycling (unless one is using only testosterone in low doses). The muscular gains alone can cause some minor problems if they occur too quickly. Other problems include acidity (from too much protien), enlarged prostrate (do not ignore this), general malaise (most often associated with dehydration and carb depletion), and a host of other annoying side effects that we all have our ways of coping with.
I find myself more and more concerned with these sides, and less concerned with being a perfect physical specimen (on the outside) as I get older. I have had the body I wanted, only to discover that it didn't change anything about my life other than what I looked like. The difference between six and four percent bodyfat is primarily a psychological one, and to the public the six percenter always looks better.
Know why? He's healthier. I know from personal experience.
Anyway, about your stomach pains. For starters, I suggest taking in some ginger to help digest your protiens. Also your water intake is a bit low. Add half a gallon. Add Tylers Detoxification Factors if you are not taking them now.
Another important consideration is acidity. This can be combated with a minor dietary adjustment. Watermelon and lemons alkalize the body, so it is a good idea to take a day or two from each week and eat these fruits, without taking in any protiens whatsoever. No, it will not hinder your gains, and in fact I guarantee you will feel a hundred percent better with just this adjustment.
Lastly you want to consider the possibility of constipation. I drink a lot of prune juice and grapefuit juice. On days I feel too full or too distended I simply eliminate protiens altogether and drink cup of black coffee followed by a tall, cold glass of prune juice (with pulp). Almost every time I discover that I was constipated beyond my expectations, even though I am familiar with this side effect of cycling. I suggest you give it a try.