Car misses when put into drive

This sounds exactly like a bad fuel pump. Do this turn the switch on then listen for the pump to run when it doesn't run have someone beat on the fuel tank with a piece of wood if the pump runs replace it. I hope this helps. Take Care.

is the motor missing or is the transmission slipping. if the motor sounds in time then I would say look at the transmission.

recheck the firing order . sounds like you have crossed two plugs

plugged catallic convertor?

Something like this is often a stuck or poorly sealing valve. A Vacuum gauge is the least obtrusive way to notice vacuum changes. If a cylinder fails to seal, vacuum will reflect the loss of compression and it will result in a bounce on the meter.

White Smoke out the exhaust, is usually a sign
of coolant & most likely the start of a bad head gasket

At this point your use of the car should be curtailed,
to prevent any further damage

You should not use the car at all, until all issues are
diagnosed & resolved

Plan on using other means of transportation

http://www.fixya.com/cars/r7030578-engine_turns_over_but_wont_start

Please see my tip for this problem. From what you say, it sounds like timing (electrical) is not correct. What is new and what is old on this new motor you put in? Knowing will help me , help you.

common causes for back firing, low fuel pressure, or restricted injectors, breakdown of secondary ignition coil, internal ignition coil arching, or a dead spot in throttle position sensor.

fuel injectors

have you tried removing the idle speed motor and cleaning it with throttle body cleaner, as well as port it is removed from?