ND played Michigan at home in 2008. The game you refer to was 2009. UM had no answer for Michael Floyd until he had to leave the game with an injury. The Armando Allen call was even reviewed by the booth and still they got it wrong.
Jarious Jackson running out of time while he was driving them for a score was indeed 1999. The irony is the next week against Purdue they ran out of time again. This time right on the goal line.
Finally, the game where Reese dropped the ball with no one near him was 2011. That was the screwiest game I've ever seen. The first night game at the Big House. ND had a commanding lead and just frittered it away. Then they looked like they pulled it out at the end, but left 30 seconds on the clock. Michigan won with the most improbable of plays.