This may be a stupid question but here goes...
May I ask why have the master unit at all? I see you have a commit that only requires the interceptor unit and some kind of switch for the digital inputs to the Arduino, this sounds like the 'master' is only interfacing with the app. Seems a lot of work and fiddling when you could add either bluetooth or wifi to the interceptor for the interfacing and get rid of the 'master'.
I have briefly looked through the source as I understand the interceptor will pick up frames intended for the haldex (on 1 can bus) and manipulate them to do what the user wants and then spit it out to the haldex to tell it what to do ( the other can bus ).
The master interfaces with the app and pulls the frames from the haldex, presuamably as error checking agasint the state the interceptor thinks its in rather than to display the current state in the app, chucks any changes made in the app to the interceptor.
Just trying to get my head around it and whether I could perhaps make this work on a single Rpi - I don't have much experience with Arduino so I am unsure if its due to memory etc to have the two.
Good work though & cheers.