Hooray - solved the problems and bought the software!
Seems to be working fine despite one of the tests in rSAP (Trial) failing (I think it's SELECT DF.GSM but I didn't record it as it all worked in the end and it is my son's phone so can't check)
As everything seemed to go wrong on every step of the way I can't be 100% certain what cured it in the end but it wasn't working for me I think I misled you - I did install using the installer but reinstalled rsap.zip using TWRP as a check.
The major changes I made between in not working and working was to reload TWRP, SuperSU and CM13.
Between us we have two more OPOs to try this out on so if I do it again I will try to record my actions in more detail.
Three weeks ago I started to see if I was able to modify the OPO so that my father could use with their Skoda Superb bluetooth RSAP module. Calkulin KitKat installation was very easy and quick. However, the next updates were very heavy and long. Even in one of them, it amended me the recovery by installing the original one instead TWRP. After several attempts at the end I managed to install all the Cyanogen official OS updates to Marshmallow 6.0.1.
Finally yesterday we got to try if the OPOPO worked in the car. And eureka, it works great! Now he can already stop using his old Nexus 4.