I can well understand how these warts and the difficulty eradicating them can be upsetting.
As to your burning pain, it does not sound to be an infection and the distribution (scrotum, back, abdomen) is also not consistent with a stricture or and infection. I would consider a pinched nerve in your spine if the pain is primarily one sided, though certainly it could be a two sided problem. If the neurologist cannot find anything, then I would look to an emotional cause and treat you with a mild anti-anxiety medication or an antidepressant.
Good luck!
S.A.Liroff, M.D.