For the two seasons Manning got to play against Belicheat in the East before realignment, the Colts were 1-3 against the Pats*. After realignment in 2002, the Pats* initially won 4 straight against them with 2 of those wins coming in the postseason. Then, from '05 to '10, the Colts went on a 5-2 run against the Pats*. So the Colts with Manning were 6-9 overall against the Pats*. The Pats* are now 5-0 against the Manning-less Colts and 4-0 against Luck. And the games with Luck haven't even been competitive with the average margin of victory being 29 points. If the old Colts with Manning got to stay in the East, I'm assuming things would have been a bit more difficult for the Pats*. Conversely, they'd probably also have been a bit more difficult for the Colts.
As for the Colts with Manning in interdivision play, against the:
AFC East (26-26, includes games from when the Colts were in the East)
North (22-4, 8-2 against the Rats, 2-2 against the Steelers, undefeated against the Bungles and Browns)
West (22-10)
South (42-13)
Looking at that, the North fared worse against Manning and the Colts than they did against Brady and the Cheats.