Sounds like cuffitus which is inflammation of the cuff or last two centimeters of anal canal. The burning and itching are all internal. Also, if your stools are loose this could cause the burning sensation. Try and bulk you stools if possible if this is the case. Your symptoms could be brought on by the pregnancy or possibly pressure on the pouch? Warm baths also will help.
I know the feeling you are describing very well as my cuffitis is chronic. Contact your surgeon who can probably see you or prescribe something rectally to help. You also should consider finding a qualified GI to assist you if you have any future jpouch issues.