Rocker cover

If the flat spot and the hard start, developed after the valve adjustment, I would go back and recheck/redo it. Possibly check your feeler gauge etchings.It really sounds like some valves are tight. The hard start could be tight exhausts. The flatspot could be tight intakes.

Getting back to the misfires.Since you didnt mention misfires prior to the parts replacement, I assume it came afterwards. In which case, I would be looking at the new parts.
The first thing I would do is figure out which cylinders are faulty, by pulling one wire at a time.When found, I would compare them first to the firing order.
- If they are consecutive firing, I would pop the cap, and look for a defect there.If none there I would examine the wire routing to look for cross firing. And then I would check the plugs themselves, by swapping them to different cylinders, and again isolating the problem cylinders.
If they are not consecutive firing, perhaps they are adjacent cylinders, in which case a head gasket blown between cylinders may have occured, however unlikely at this point.
Perhaps the two misfiring cylinders are next to eachother on the intake manifold. In which case the problem could be a gasket there.
Perhaps the two are on the same idle mixture screw(2 BBLs), in which case I would be checking out the airbleeds, and idle circuits.
Perhaps the misfires are random and untraceable to particular cylinders. In which case I would be looking to the AFRs,the fuel quality/age, the intake again, or air contaminated with EGR.
And as a wild card, dirty points. If you have them, they should be the first thing on the list.
So, as you can see, it all starts with determining who the cranky cylinders are or are not.
Good luck, hunting.