I know this is going to sound strange, and it may or may not help the issue - can't be sure - but a number of the symptoms you're relating could be the result of someone with undiagnosed celiac problems. That's a problem with the ingestion of gluten (wheat, rye and barley - sometime oats). B12 problems, hair loss, tremors and extreme fatigue can result from gluten issues.
You may want to due a bit of reading on the subject to see if the overall picture 'matches' some what what you've seen in the past, and what is presently going on.
You want to know how come you are not better. You ask if your tremors or cyst could be contributing to your digestive problems. Questions about that pineal cyst can be better answered in a brain disorder type forum, but I do know that those cysts can affect hormone levels in the body. Your age of 51 also suggests menopause hormonal changes are figuring in there, as well. Thus, you may want to consider hormone replacement, whether natural or otherwise, in which case you can visit a menopause forum for suggestions of natural ways to counteract hormone changes.
The medication you take for your tremors, check the side effects of that drug, or any other drugs you take, see if tummy upset is one of them, and perhaps you could get another drug that would work better. If nothing else, always take any pills with at least milk.
Overall, I would say that your digestive lining has either been rampaged by the viruses, or as a result of a general acidic environment, and/or some other malabsorption process, and thus you are not able to assimilate nutrients as well as you might. Since you have been treated for the viruses and you have had the irregular growths in your bowel removed, you are at least starting out with a fairly clean slate. So, that leaves a possible remaining acidic or malabsorption chemistry at work here.
Malabsorption can be caused by so many things, that only a gastroenterologist expert can decide how to medically treat such an imbalance. It sounds like from what you've said, that the injections of B12 might be part of what they've decided to do, to counteract that. You can always consult various websites that are dedicated to malabsorption issues, to find out if any of your symptoms seem to apply and how they can be treated...most of those websites will offer natural ways to do it, along with standard medicine. Usually if you Google the words of your problem, like malabsorbtion, along with words like treatment and causes, you will find health websites that will come up over and over again, and will feature a variety of diseases and a step-by-step explanation of how to deal with the disease. I would do it for you, but I'm short on time. Seems like www.emedicine.com or something like that is one of them, but some sites are better than others.
For an acid digestive system, you say you watch what you eat. So I can only suggest a few more natural things to help that, in case you haven't tried these. First of all, if food hangs around in the digestive tract too long, you'll get acid. So, you want to keep your bowels moving as regularly as possible. One simple way to accomplish this without a whole lot of diet changes is to add 100 percent whole wheat bread to your lunch and dinner. Start with just one piece of bread a day. Find a store brand or any brand that has nothing but whole wheat in it; which means no extra nuts or seeds in it. Just plain brown bread with "100 percent whole wheat" on the package. Also, drinking some extra water every day as a regular thing helps digestion, as does ordinary exercise several times a week. The bread will also tend to soak up excess acid.
Also, if you will eat cereal with acidophilus milk and no more than 4oz of orange juice every morning, what you get is "replacement" vitamins from the cereal, "good" bacteria to help break down waste from the milk, and daily maintenance and "repair" of the muscus membranes with the juice.
I hope some of these ideas will help you think about your situation in new categories that will lead you to some fresh answers. I am sorry you have had to go through this ordeal, and I know you must be pretty scared by all this. But hopefully even a little improvement by just one thing someone says in these forums to you will help.