Let me start by saying I have worked with lead acid batteries for several years, but I am not as 'expert' as some in the club. But, I'll try:
The battery pack in the Ranger does not want to charge lately. The "fuel" gauge (SOC) shows 3/8. The Distance To Empty shows 25 miles.
You are relying on a gauge that has been programmed to approximate the SOC under good or ideal conditions. I have yet to see one that tells me anything reliable when the batteries get real tired or unbalanced. Individual cell or individual battery measurements are much better when the batteries are bad, and the one meter for the pack is not very useful. I would recommend you not even waste the time to look at it. It just isn't going to give you any useful information.
I popped the caps off the batteries and connected my 10 amp 12 volt charger to the batteries one at a time. I watched each cell make bubbles. Each battery was connected for a minute or two.
I think you likely brought them up as far as they will go with a charge. The two standards are the resting cell voltage and the specific gravity of the acid in each cell. Ideally you would measure all cells for Sp. Gr. and all cells for resting volts at full charge. Since cell volts are somewhat difficult to get, battery voltage at full charge will likely tell you what you need to know.
There was some variation in the level of acid. I could see some solids floating in most.
There shouldn't be any solids floating. They should bubble when you have them fully charged and apply excess voltage trying to charge them. When they bubble, they give off water, and some sulfur oxides (in fumes) The sulfur oxides can be detected with your nose, and will deposit on surfaces near the battery vents. Because those sulfur oxides + water make surfuric acid, you should wash the batteries regularly with a dilute sodium bicarbonate solution (baking soda) and then clean them again with a detergent solution. If not washed off, the sulfuric acid will form electrical 'tracks' allowing small amount of charge to escape and your meters will begin to detect a 'ground fault.' Keep the battery tops and containers really clean.
The best answer is to keep the fluid level in each cell so that it completely covers the plates. It really doesn't matter if it covers the plates by 1/8 inch or 1/2 inch, what does matter is the specific gravity. Before you start adding distilled water, check the specific gravity of any low cells when they are well charged. Use a hydrometer to check each cell, and use this chart:
The following shows the approximate state of charge at various specific gravities at 77ºF / 25ºC.
Charged Specific Gravity
100% 1.265-1.275
75% 1.225-1.235
50% 1.190-1.200
25% 1.155-1.165
0% 1.120-1.130
Hydrometers are at best accurate to +/-0.005 points. Voltage can be used to estimate state of charge, however caution must be taken when interpreting voltage readings.
When I was done, SOC 3/8, DTE 25. The few that I checked were about 12.9 V less than an hour after charging.
The voltage of a '12 volt' battery at full rest is about 12.7 to 12.8 volts. Your meter may read a little differently, but I suspect they had not equalized yet.
Is this what's to be expected when letting a set of batteries sit neglected for 3 years?
Actually, these are much better than most I have seen.
The pack seemed to come back to life for a while but they're acting worn out now. Is there a file or a link to the basic knowledge I need?
The club used to own some paperback books that were the best source. Battery University also does a pretty fair job
http://batteryuniversity.com/learn/article/lead_based_batteriesWhat's the voltage of a fully charged 12V battery in good condition? That kind of thing. Costco has deep cycle battery size 24, 85 Ah for $72.99. They can order 26 with all the same mfr date. Is it time to change the pack again?
I suspect a couple of things. Likely your batteries are significantly sulfated, and some of this is reversible, some is not. The fact that the 12V batteries all measure more than 12V is a good sign, indicating no dead or reversed cells. I might suggest a strong desulfating regimen, as it might work rather than immediately spending a couple of thousand dollars on a new set.
Take some time and see if they can be brought back with a desulfating charger.