Q: Engine takes to long to warm up I've replaced thermostat already and it misses horrible till it warms up its a 4.9 engine

This engine uses a cooling fan clutch that controls the fan speeds on demand when the engine radiator starts to get hot if increases air flow to cool the engine down and slows the fan when it needs to increase the engine speed. If the fan clutch is locked up then it will not let the engine get warmed up. With engine cold and engine off see if the fan clutch allows the fan to spin pretty free with little resistance. If it is hard to turn the fan then the fan clutch needs replaced. For the rough running your engine running colder than normal will build up carbon deposits on the valves and foul out spark plugs. The carbon build up on the valves will absorb fuel when engine is cold and cause runs rough and misfires. You will need to de-carbonize the engine after cooling system repairs and may even need to have a major tune up done to correct misfires. A mechanic like one from YourMechanic can do all the repairs and diagnosis needed for you.