Hi,
I assume you plan is to do this entirely in VHDL or Verliog, right?
Are you familiar with state machines? They provide an excellent way to implement this sort of sequential logic in VHDL or Verilog. Google should spit out tons of articles about that topic.
So I'd suggest you first implement some counter that generates a single pulse every 3 s. Then your state machine listens to that pulse, and whenever it receives one, it switches to the next state which generates the next letter.
In order to do that, you should have an entity that drives all signals for the LED matrix, and has some inputs that let you select letters. I assume you already have something like that (i.e. if-this-signal-is-applied-then-display-a-capital-A-otherwise-display-a-capital-B, something like that).
It's very likely the easiest if you separate your design into at least those three entitites (counter, state machine, matrix driver).
Best regards,
GooGooCluster