You can do this manually or use ezremaster which will I believe create exactly the tool you're looking for, repeatedly.
I've used ezremaster frequently to create ISO's which boot, then run specific interactive applications from bootsync.sh. The whole process takes but a few minutes, maybe a couple more when an application needs updating or changing.
having said that, I haven't used it since tc-5.1 was released, but 5.0 worked great so no reason to think it's performance would be any different in 5.1 and is in the repo.
I have to thank Gerald_Clark for pointing me towards bootsync a while back, which solved my root interactive issues. Only caveat is that any application which runs from bootsync runs asynchronously, therefore must terminate. right Gerald??