In Duan Yus first encounter with Murong Fu, even with 6MSJ and WYY's guidance, he wasn't able to fully overcome MRF.
However, during DY's fight with MRF at Shaolin and afterwards, Jin Yong clearly states that MRF is no match for DY and even the likes of XF would have a very hard time facing DY, despite DY not having gained a significant amount of internal energy. Although Bei Ming Shen Gong will give him a steady growth of internal energy, he had not yet absorbed Jiu Mo Zhi's energy at that time. The amount gained from Bei Ming Shen Gong in just a few years should be negligible compared people at the calibre of MRF, seeing as how Wuyazi has what . . . 70 years of it.
So what exactly happened in the two or so years between DY's encounter with MRF at the mill and their fight at Shaolin?