I'm Dr. Clark and I'm happy that you have asked me to assist you with your child and hope that you can benefit from my many years of helping parents like you.
You are correct that lumbar punctures are common procedures and they do not cause much pain, even at the time it is done, and certainly not later. You may give him calpol for his discomfort since he does not have fever.
Since he had the procedure done I assume he was ill and therefore I would think that his crying is just due to his underlying illness.
I see you are still offline so I'll exit chat but be available should you have questions.