There seems to be some conflicting information/confusion of terms.
Firstly a lead acid battery will self limit its charge to something close the amount of charge used, e.g. if you've used 80Ah then after a short while the charge current will be 80A or thereabouts.
Secondly the reason most batteries die is sulphation which is due to inadequate charging, so better to 'abuse' your batteries with high charge rate than leave them not fully charged.
Thirdly alternators weren't designed to charge massive banks of domestic batteries, they were designed for cars to replace the tiny amount of charge used to start an engine and then provide power to run everything electrical thereafter, without help it will struggle to fully charge a well used domestic bank in a reasonable time. That's where the A to B device helps by boosting the 13.8v (more likely 12.5 under load) to around 14.5 to charge the batteries in a shorter time.
When calculating max charge a rough rule of thumb is thus:
Alternator rated current x 0.8
If using an A to B giving a 20% voltage boost including losses. x 0.7
Unless you have seriously large cables joining all this up x 0.95 for cable losses
Putting all that together you have a max available current of about 55% of the rated alternator output, subtract your electrical load from this and there what's left to charge the batteries.
As regards diagnosing your particular problem I recommend investing in a cheap DC clamp ammeter for about £30 that you will use time and time again and is the best way to find this and similar faults.
Measuring Ah in and Ah out is a really good way of assessing battery state as a lead acid battery is close to 100% efficient if you measure this way unless overcharged, it is not 100% efficient if you measure Wh in/out.