ideas please guys

Hi guys ive finally put new smf and new engine in but getting some judder when on light throttle about 2k revs could this be from unplugging the throttle body and also cleaning it out? Before anyone says it i gad to unplug it to do engine change. Ive had a snap on code reader on it and cant do much but says throttle is at 4.7% with ignition on but no engine running. Can anyone verify what it should be or diagnose my problem?also when started in morn and the choke is on it missfires until warm enough or if i slightly raise the revs