2000 Ford Escort Crank but no start

Engine Performance problem
2000 Ford Escort 4 cyl Two Wheel Drive Automatic 74k miles

This car was running rough like it wasnt running off of all cylinders so we did a tune up, (plugs and wires), and replaced the pcv, and the pcv hose because it was clogged. After we did that, it was still running rough. The thing is is wouldnt idle. It would shut off if I let up off of the gas, and then be hard to start again. As I got out to check the catalytic converter, I saw that it was red hot, so we replaced the cat. After we did that the car cranks but doesnt start. I put air to the valves and felt air coming from cylinders 1 and 3, (is that normal?), Through the exhaust. These are the repairs we have done. I used a scanner and the codes it gives me is misfires on cylinder 4. If you could can you help me with this problem. I would greatly appreciate it.