Their FA Cup run was hard it inc games against Liverpool (4th round) and Chelsea (a 1/4 final which went to a replay) then playing Arsenal in the semi-final, those last two rounds were against teams they were still competing against for the title.In 1999 did they get more points than City this season? Did they beat better sides in the two cups?
CL however is different. They qualified from the group stage as the second best, second placed team. They beat, on paper, good Inter, and Juve teams...although at the time both were having shocking seasons in the league, finishing 8th a 7th respectively.
If my memory is right, Bayern should have won that final comfortably.