Just finished reading the whole thread. Very interesting, but i have a feeling that i may be a bit more tricky on a modern vehicle that probably already implements algorithms similar to this. If anyone know how they do this, i would be very interested in knowing.
Looking from a completely different side, the reason your deep cycle batteries cannot fire up the car once they are low is because they cannot generate enough current. If one were to add a capacitor bank in parallel then even almost dead batteries would be enough to fire up the car.
Like this guy:
I am pondering, on a modern car, would it be beneficial to remove the battery completely and use capacitors instead? You would not have the problem of charging a battery that lost capacity if not used for a week or so. Also you would not waste energy on a battery that started to age. (you would need means of charging it (which is very quick ~1-3 minutes) if left for a couple of days).