I'd be looking at
- spark plugs and coil packs
- fuel pump and fuel sending unit
Either the misfires are caused by a lack of fuel or incorrect/poor ignition. Were the plugs/coils changed when the engine was swapped? How many miles on the swapped engine since last ignition refresh? Does the car sit a lot? Has fuel pump ever been done? The two times I've seen misfires on my '03 S were both of those things. A new fuel pump & sending unit & filter (plus a clean out of the fuel tank due to varnish buildup since it sat for too long with the PO) cured the first, fresh plugs and coils cured the second instance. Might want to check out and clean the throttle body too, just in case there's crud built up from a previous bad AOS.