It all started when I ran out of gas

To make a long story short I ran out of gas, after I put gas in tank it would not start after three days of checking fuses, relays, fuel filter, and fuel pump and having it towed I finally get it started by pressing on valve. Now the car starts and runs good but there is a knocking noise which at first I thought was come from the engine, but it is coming from the case that is around the timing belt. Any ideas what I should do?