From the description of the under hood wiring , it sounds like not much if anything was removed from the original system and the injection system and ECM/PCM ( depending on what year system was installed) was just installed over it . About the only wiring that comes to mind that may have been borrowed for the new system may be the charging system . Even that would have to be upgraded since it's likely the older system would have a lower amperage output and wouldn't be adequate to run the injection system and all its sensors . As a suggestion , it may be best to follow all of what currently connected and find if anything isn't connected . The old system was just an ECM which were mounted under the dash , a dura spark module and distributor , an electronic feedback carter BBD carburetor and what draw the ECM needed from the alternator which may have just been a simple junction . Regardless of what year your cj7 is , it is best noted to follow what year , make and model the ignition and fuel system was liberated from to help follow a basic diagram to insure that all is complete and that anything else found will be verified as not part of this current system . Wondering if any of the original wiring was borrowed to complete the install and the wiring gauge is not up to spec ? If the job was done correctly , that shouldn't be an issue but shouldn't be overlooked .
P.S. - although the painless systems are nice ( and $$ ) , agreed , it may not be necessary in your case . Inspection of the system will verify condition and completeness . But even so , it would be hard to order a new system since your jeep is no longer stock so that may only leave you with aftermarket and not original equipment.
