Very little B12 is absorbed orally. That is why you take a huge dose so a few micrograms will get thru. Not likely to cause anything noticeable at all. Doctors typically don't test intrinsic factor anymore (Schilling's test--most labs stopped offering it)
There is a test for antibodies to stomach parietal cells to look for autoimmune issues.
http://www.nlm.nih.gov/medlineplus/e...cle/003351.htm

You could be shakey due to low blood sugar, in the morning.

You can try something for foul smelling GI issues. Get some Psyllium seed (either powder or the capsules) Take one or 2 capsules daily to start with alot of water at mealtimes, and see if they work. Say one for breakfast and one dinner.
They will absorb any toxins in your bowel, that are causing you grief (smells and IBS type symptoms). This works very well for minor bowel disruptions. You may find you can eat better after a couple of weeks of this. Also look at your sugar consumption. Fructose can cause lots of gas, as well as sucrose, because it feeds Candida. Stop all sugar and fructose for 2 weeks and see if the gas is better. These are two common causes. If this does not work, you'll have to think of something else to try.

You may need some good probiotics ultimately, but try this simple inexpensive thing first.