Mike,
Mike, I agree with Joe that what you have are two separate banks which can be combined when you put the switch to the Both position. In that setting it will be a parallel connection. When 2 12 volt batteries are hooked together in parallel the voltage stays the same but the amps hours of the two batteries are added to each other. If they are hooked together in series the amp hrs stay the same but the voltage doubles to 24 volts.
Generally a battery will have two ratings: the Cold cranking amp (CCA) and a 20 hour amp rating given as amp hours. As long as you have batteries which have a high enough CCA to start the battery your next concern will be how many amp hours the batteries can deliver. Sticking with a Deka battery as Ernie mention a quick search indicates a Deka DC27 Marine DeepCycle group 27 flooded battery is listed at 625 CCA and a 20 hour reserve of 90 amp hours.
Recommended alternator sizing is the alternator should output approximately 25% of the battery capacity. The 20 group 27s have a combined capacity of 180 amp hours so the 55 amp alternator falls with in the recommended size. The charge acceptance rate of flooded lead acid, AGM and Gel batteries drops as the batteries reach about 70% full. At a 50% state of discharge a 90 amp hr battery might accept 20 or even 30 amps but by the time the battery is a 70% state of charge it might only take 10 amps and by 85% state of charge it might only take 5 amps. What this means is it takes a long engine run time to fully charge those batteries.
A solar panel or two would be a good addition to your system. Ideally you would like enough solar capacity to keep up with your daily needs. Unless you crank up the stern really high it is likely that your autopilot is the big draw on your system. I have no idea how much it draws. You will want to look at the specs for it and multiply that by the daily usage to come up with daily amp hours. A rough guess would be that your total daily draw is in the 20 to 25 amps.
Probably starting to get to much detail here so I will try so stop myself.
To keep your lead acid batteries happy you should not discharge them below 50% and you should try to bring them up to full charge as quickly and as often as you can. Solar is the best way to do that considering your usage. You can find charts that will show you how many amp hours or watts you can expect out of a solar panel in your area (maybe 15 to 20 amp hrs a day from 100 watt panel). If you are mostly day sailing you don't need to put back in the full daily draw because the panels will continue to work while you are away from the boat. I will disagree with Ernie to the extent I think you should always have a controller for solar panels to protect the batteries. Spend the bit extra and get a MPPT style as opposed to a PMW. Try to find a location for mounting that gets the least amount of shade.
Based on past experience it appears the two group 27 batteries meet your electrical needs. You should replace both batteries. The banks are separate so you can get away with using batteries of different age but because you combine them at times it is better if they are the same age. To keep it simple I would suggest you stick with two group 27 flooded lead acid deep cycle. Just make sure you keep the water level topped up using distilled water. You can upgrade to AGM batteries without any changes. AGM and wet cells have to same charging requirements. If you go to GEL batteries you will need to change the charging rates.
Two benefits of AGMs are a slightly faster charging rate and no off gassing during charging. If off gassing is not a concern I suspect you would be better off with flooded wet cells. I have AGMs because my batteries are under the quarter berths and I don't want the off gassing. If the batteries were in a back locker I would likely use flooded. I guess a third benefit of AGM batteries is that you don't have to top up the water. You do have to be careful with AGMs, most manufactures of AGMs tell you not to do a conditioning charge. Conditioning charges are over 15 volts an can boil the fluid out an an AGM.
You need to buy a digital multi meter and spend a little time learning how to use it. The readings you are getting from your current (pun intended) meters are wrong. I have added a chart showing voltage for lead acid batteries at various states of charge. If you search the internet you will find many such charts with slightly different numbers but generally a 12 volt battery at 11 volts is basically empty. You really don't want them to go below12 volts. Generally the charging voltage for lead acid batteries is 14.4 volts. For Gel batteries it is lower. A fully charge and rested 12 battery will normally give 12.8 volts. You will want to check at the battery terminals.
Your questions:
1: yes the 55 amp alternator is big enough and a bigger one is likely wasted.
2: CCA amps will not change the battery state of charge and going to 400 would not be a good move. If the batteries are a bit weak they may not put out enough to start the motor. 600+ CCA gives you a cushion.
3: Stay with the group 27 600 CCA deep cycle batteries. It is better to have the batteries both from the same manufacturing batch but at a minimum it they should be manufactured with 6 months of each other. If the budget does not allow replacing both you can have different ages because you generally don't combine them.
4: AGM. You can with to AGM with no changes. I am not sure you will get enough benefit to justify the extra cost. See my comments above.
5: Do you mean chemistry or maker? I suggest a good quality flooded deep cycle group 27. You won't need to change cables or battery tie downs. Good AGMs are expensive now and you might have to change the cable ends to connect to the battery posts.
6: Very difficult to answer. Decent panels with combined capacity of 25 to 200 watt with 75 to 150 watts being your sweet spot between capacity, cost and size. Definitely MPPT controller for each panel.
Hope that helps.
Sorry no time to proof read.
Mark Powers