Sorry, been away and just seen your reply - hopefully more members will get involved with a diagnosis.
Stating the obvious, it sounds as though its rich. So plug colour check and if plugs are darker, its the slow running circuit - air screws/passage ways, primary jet size/blockage but from experience of trying to sort out the low speed running of my CR750 Rep, don't discount mains/needle positions as from previous posts on the subject (someone on here has a chart that showhow all the jets/circuits affect the running across the range) the needle position can also affect across the range.
I know that you will feel confident that all was checked and assembled as per spec but (and from personal experience!) there has to be something amiss - so a recheck of the carbs seems the starting point.