Check engine light is blinking in my 2000 Honda Civic EX, also is running rough, could it be the cad. conver?

Don't go to the auto shop. Go to Autozone and rent a OBD2 scanner for $100 deposit. You will get the money back in full when you return it. Plug it into the port under your dashboard and hit Read. It will tell you the code and maybe the problem. If it just shows the code, look the code up on google to figure out the problem. So basically this will cost you nothing.