The manual for your motor should give you the specs for the required starting battery. The group 27 battery is probably sufficient. I agree that rewiring the system so the group 27 is your starting battery and the the two 4Ds are your house battery makes sense. You don't want two house banks, just one large one with an simple on/off switch. Use your 1,2,all, off switch as an interconnect so you can start from the house bank if needed. There are many ways to set up your batteries, but this is a common, modern approach.
Following the steps in the Link 20 manual for battery capacity testing should give you an idea of the health of your batteries. If the actual capacity is was off from the advertised capacity you batteries are on their way out.