If it's only running rough when you first crank her up I would say look towards the temp sensor which is below the thermostat.
Might check all the vacuum hoses that can cause one to miss and have little power. You have a healthy engine with that kind of compression. How long have the plugs been in there-you did put new ones back-right? Could be a number of things from the crank sensor getting ready to go-mass air meter-throttle body sensor-might try unhooking the mas air meter then cranking the car back up and see if anything changes-also try the same with the throttle sensor-you will have a code thrown as soon as you unhook one of the sensors, so be ready with your scanner to reset the code after you hook everything back up.
The first thing I would do is to clean the idle valve located on the air bonnet just next to the throttle body-that can make one idle funny also.
Most time when you have a cylinder misfiring there will be a code to tell which cylinder is weak. Check all the vac hoses very carfully-also check the vac tree that all the hoses hook up to on the intake-there is an o ring in there that can leak air also-but probally not as much as to cause your problem.
There are power stages that can go bad as well on the front side and back side of the intake that handle 3 cylinders each-if you can tell which cylinder is giving the problem you could switch the pwer stages and see if that moves the miss to another cyl then telling you that in effect that it's a power stage.
Good Luck
Poolman