Since you have a Scanmaster you should check BLM, INT, O2 cross counts at idle and during the time the issue happens, then check to see if you have vacuum leaks, especially after the MAF (un-metered air) if something seems amiss. Also check the grounds at the cylinder head.
There's lots of other stuff to check, including mechanical stuff like a broken or worn valvespring, EGR issues if it is hooked up, dirty injector, clogged or dirty fuel filter, cam sensor, crank sensor, etc.. Also, if the misfire is only under load (driving), or if it can be reproduced by bringing motor to the rpm range you experience out on road but in park (no load..), etc...
If none of the easy stuff pans out, mebbe post the Scanmater values at idle and someone who doesn't just sit on their duff all day and eat/watch TV like me can help..
No codes stock mass air checked for vacuum leaks fuel filter is new injectors are new . I don't know about ignition module seem ok when I replace coil checked connections . The o2 does seem a little slow to respond on scan master .