Not speaking from experience as I have never rewired a CJ , but any electrical work I've done or do , I always document . I would first lay out the replacement harness and compare every connection that it is truly a direct replacement and that all connections and circuits will be complete and that there will be no voids . If there is anything different or incomplete , you want to know about it before you tear down so you have a plan to deal with the missing item(s) or change(s) you will have to make. You really want to know this installation will truly be plug and play knowing where every connection will go and is complete when it's go time . The last thing you want is stop cold right in the middle and have the project sit until your ready to resume .
The reason I say this is because electrical being complicated enough as it is , you want to do everything methodically moving right along and NOT forget a step as you have planned .
Projects that sit too long waiting for completion have strange things happen to them . Things disappear , get altered or disturbed with no explanation and then you get set back and frustrated , ending the joy and positive thinking that would have completed an "EASY" project.
Im sure your CJ is your prized pride and joy , would not want you to be disheartened just because of glitches . Really , if you take pictures , make notes and diagrams as you feel the need , you will thank yourself later . Disassembly will tell the story as you will compare the differences, if any , and praise the similarities that will make you happy and confident all will go well .
when you start breaking it down , there will be no one more qualified than you to complete this job right as no manual or text will be more complete than your own two eyes and hands .
No book can walk you through this job , even wiring diagrams and schematics vary with the different models and options so only you will know this job best . That is why you would not want to stop in the middle and continue another time , you want it fresh on your mind to complete it right . Not trying to question your ability , you would not even take this on if you did not think you had a chance to complete it , just that every wiring job always starts off with the thought ; " I'm just going to remove the old and install the new ". Dosen't seem to always work,out that way . If you document as complete as possible , I know you'll finish it the way you want , the right way . Wishing you best of luck and a great running CJ soonest . Greg