I imagine a lot of guys on here, who know sytys way better than me will recommend going over everything with a fine tooth comb...state of tune both hard parts and ecm prom set up, checking vacuum lines, verifying balancer hasn't slipped, verifying ignition timing, fuel pressure, and data logging it if it still has problems.
I've had hesitations on my Sy from fuel pressure being too high at idle, low injector voltage from ecm, plug wires that were grounding out, dirty ground wire connections, down pipe hitting frame and tripping knock sensor...you name it.