I would hook the other 2 batteries back up and built a dedicated bank for solar energy for several reasons. Firstly, diesel engines draw a ton of current when cranking over, even more so when its cold out. Once it starts to get below 40 or even 50 degrees out one battery may not be enough to start the bus and it will be really hard on that battery. Even diesel pickups have two batteries. The batteries also help buffer the electrical loads in a vehicle before the alternator increases its output. Engineers paid more than me believed that three batteries were necessary for safe reliable operation of your vehicle and the previous owners of the vehicle agreed enough that they didn't try and save money by going to two batteries.
Also the chemistry in those batteries is designed for high output in a short amount of time and they do not appreciate being used past a certain percentage or the life of the battery decreases. IIRC its only about 20% discharged for lead acid starting batteries. Deep cycle batteries are designed to provide less power over a long period of time and can be discharged further without significantly affecting battery life. Also two group 31 batteries (the standard heavy truck battery) isn't a lot of available power, what do you plan to run with them?