I just switched out my shortblock due to the fact it had a rod knocking. Well when we put it back together we had problems with the timing but figured we put it back together alright (using ford companies specs on timing procedures). AT first start up we had miss firing. Then we set up the timing again, same thing. After that we found a different paper on how to do it. We started it up with nothing put together except the cam sensor, crank sensor, and all the wiring hooked up and it ran fine. what else could cause the miss firing and running rough?