Edit: To be clear, this shows how to do this for a Revo, but the procedure is the same for other FC's.
I generally run the setup wizard one time, and from then on use the Configuration tab and set what I need to set.
If you run the wizard again it will set the motors to 1->1, 2->2, ...
First use Vehicle tab to set motor 4 to use channel 5 as in attachment "motor output channel5.png" (and Save)
It sounds like you need to do a manual ESC calibration (take props OFF!). Do it before proceeding.
Then go to Output tab and set Bank(channels) Mode and Update Rate for #4 (channels 5 and 6) to match #1,#2,#3
Note that this may be different for other flight controllers. You need to make sure that channel 5 Mode is the same as 1,2,3. The numbers in parenthesis are the channel numbers you need to match.
Set Max on VTOLMotorSW (the motor you moved) to match the others. then set Min, then set Neutral (about 1020 for you). See attachment "output channels.png"