1994 dodge shadow engine swap 3.0L 5speed.?

ive had this dodge shadow about a year and a half. my throwout bearing was going but i wasnt gonna tear the motor out to just change it unless i was putting a new motor in it. So i bought a motor from a junkyard it came out of a 1995 chrysler lebaron with only 60,000 miles on it. i bought new clutches, new water pump, new plugs and wires, and distributor. and tore the old one out and put the new one in...which went pretty damn well and i was happy with the job. it fired up first try but i have a miss. not a constant miss but a hesitation. it seems to clear up over 3000rpms. but not always its weird. does anyone have any suggestions or anything on what could be wrong. i really need this car to run. i like it alot. its been a damn good car and i wanna get atleast another year or 2 out of it. so PLEASE anyone. thank you for reading