Did you have the mixture set with an exhaust gas analyzer?

I had the same symptoms as you're describing, slight misfire around 2500,
then ok above that. Failed smog, replaced cat and had the mixture set (not
just the idle air screw, the AFM wiper arm too) and no more misfire.

Of course this could be many things. But I mention this because I watched
them set the mixture by revving the engine to around 2500-3000 rpm, and I
could hear it even out as the mixture got closer. YMMV.