What would Cause my engine to have a low rev?

What would cause my rev to be low? I just replaced the head gasket, timing belt, and water pump. While the engine was apart I noticed that my vacuum switching valve and my thermal vacuum valve was broken. I replaced the plugs and plug wires. My engine red lines and limits the rev and about 6.2 rpm usually. Now it stops and around 5 and sometimes stalls. The car has a lack of power and often misfires. What could possibly cause this problem? I checked the time marks several times on the crankshaft pulley and the camshaft pulley. I have not checked the timing marks on my camshafts. I also get a code for my knock sensor and my throttle position sensor.