I've got a different thought. It seems to me it could be a warped rear sprocket. If the chain was way too tight and you rode it for a while, it could have got the sprocket hot enough to wear and tweak it out of round. Hence, it would only be noticeable under load. Together with a suspect, overstretched chain, I would bet that you will have to change sprocket, chain and front sprocket to get rid of it.
