Thanks for using the forum. I am happy to address your questions, and my answer will be based on the information you provided here. Please make sure you recognize that this forum is for educational purposes only, and it does not substitute for a formal office visit with your doctor.
Without the ability to examine you and obtain a history and review your imaging, I can not tell you what the exact cause of your symptoms is. However I will try to provide you with some useful information.
The movements, the jerks, you get in your arms, if they are a sudden loss of muscle tone followed by rapid recovery, could be caused by asterexis, also known as negative myoclonus, which is most often due to metabolic problems, such as liver problems, but can occur in other conditions such as liver dysfunction, or due to infections, or medications.
The episode of confusion, lack of comprehension, could have been related to your pneumonia; in some people, something like a pneumonia can really cause confusion, and this could have exacerbated your myoclonus as well. This is called medically a metabolic encephalopathy. I am not sure from your above report if the small vessel stroke on your MRI was acute (new) or old, but a small stroke can sometimes cause significant symptoms depending on its exact location. People with Crohn's disease can have a tendency for blood clotting, and when appropriate should be on a blood thinner such as aspirin.
Another possibility is that you were have seizures, not the seizures that cause convulsions, but rather either myoclonus or confusional episodes. This seems less likely but is still on the differential diagnosis.
I do recommend that you be evaluated by a neurologist if your arm jerks persist and/or if you have other symptoms, so that the cause can be searched for, and also, if you did have a new stroke on your MRI, to ensure you are on the appropriate stroke-prevention therapies.
Thank you for this opportunity to answer your questions, I hope you find the information I have provided useful, good luck.
Thank you so much for your input. I am taking my scans to see my chiropractor today (he was a radiologist before a chiropractor) and I will take your suggestions along. I am seeing my GP next week and will take them there too.