New to TimeQuest... Need help to add constraints and delays!

Use SignalTap. It's getting down and dirty, but it should always lead to the problem.

First place to look is probably the FIFO. Does your logic monitor the full/empty flags? They can be squirrelly, and if the logic doesn't adjust, that's the type of thing that leads to extra/missing bytes. Just a thought. I doubt this is something that can be figured out over the forum.