Here is an unbelievable MAC fact. Since 1989 (13 seasons), only 5 different schools have won the MAC. They are as follows:
Marshall (5 times) 1997, 1998, 1999, 2000, 2002
Toledo (3 times) 1990*, 1995, 2001
Central Michigan (2 times) 1990*, 1994
Bowling Green (2 times) 1991, 1992
Ball State (2 times) 1989, 1993
Looking at those teams when they won the MAC and their record against ACC teams in those seasons:
Toledo = 0-0 (no games played ever)
Marshall = 1-1 (beat Clemson 13-10 in '99 and lost to UNC 20-15 in 2000)
Bowling Green = 0-0
Central Michigan = 0-0
Ball State = 0-0
Most of those games you listed were against MAC teams that are not very good. The exceptions are:
Marshall's games in '99 and 2000
Miami's win over UNC in '98
Wake's win over Northern Illinois in 2001
I noticed that Northern Illinois' win over Wake in 2002 was not listed. Neither was Miami's win over UNC in 2002. Both of those games were against quality MAC teams.
So quality MAC teams against ACC teams since 1989 are:
4 wins for the MAC and 2 wins for the ACC. This proves that there are some MAC teams that can beat ACC teams on any given day.
I am not crazy enough to say that the MAC is better than the ACC though. Only Marshall fans are that crazy!