It's important to get the squish right, but having the squish out of spec won't cause the running issues the OP is complaining about. I'll also add that a flat spot around 5-6k is almost to be expected with chambers. If you're jetted right, it's not very bad, but it's still there. RZ crossover manifolds are supposed to help some too, someday I'll get some.
I wouldn't bring her home to Mama, but Mama ain't home tonight.