I am thinking of buying a madone 5.1 (54cm). It does not include the fork, but I have an option to purchase a fork off another 5.1 (same year). However, the fork is from a 56cm. Is there a major or any difference in the 2 forks?

Not a problem. You just may need to have your LBS to cut the steerer tube to your size if it sticks out too much.