What didn't work was the airframe, or certain parts of it (if ever there was a case of "If it looks right....) and they kept finding bits that needed further mods to get it to "fly right". The joint trials team will tell you that it was working, very well; it just needed some more work.
Of course it was also
such a good idea to install high-ratio bypass engines deep within the wing structure, with very long inlet and exhaust ducts. The effect of a single fan blade failure would have been catastrophic, both to the airframe and to the mission crew.....
Brilliant mission system, frankly appalling airframe.