Sounds like you have a parasite drain somewhere or your alternator is not doing a full job. Smart Battery chargers like the ctek are good as they have recondition cycles with peak loads for specific periods. It is a much more comprehensive charge than what an alternator does. You should not have to charge the batteries from a separate source everyday and simply is a pia.
Speaking from a 2h and old tractor prospective, the Rule of thumb is as big as what will fit! The more cca, cold crank amps, the easier the engine starts, the starter shall only draw what it needs. Group 27 or 31, sounds about right. There is a myriad of battery choices some swear by caterpillar, some optima..some recommend dual purpose cca and deep cycle combined, like yellow top optima or marine batteries.
I tend to separate my starter battery from my aux battery with a solenoid. Even bypassed my driving lights wiring to run off the aux instead of the starter battery. That way I kind of cheap out on my starter and get something run of the mill with good cca (at least 700+cca), you can get 1000cca) but I spend up on the aux which is a dual purpose, just in case my starter battery dies I can still use my aux to start. At present I have a yellow top which is pretty good so far 3-4 years for my aux. I think batteries use to be better in the past though, would last 8 years+.
Most battery companies would have your engine listed and matching battery, or battery dealer. If you ask which brand ?, that opens a big can of worms. Companies change ownership rapidly.
I can imagine the alternator/regulator trouble you recently had caused battery problems. Probably did stress your batteries.
In my old bj40 my regulator fried at night once, the lights went really bright for awhile then the alternator fried then the batteries stopped charging, then the lights went dimmer progressively as my batteries lost charge and then, they also died...it got expensive for something easily monitored with a cig lighter volt meter, one for each battery. Reg, alternator, batteries$,$,$. I learnt a good lesson from all that.
If you do not monitor alternator charge you risk killing your batteries. They should never get as low as 4.6v, if the battery gets so frequently drained it shall shorten it's life span. Many batteries have a memory, so if left discharged , it remembers the low voltage as being full. You want them fully charged all the time. Constant vigilance!