Don't waste your money on a capacitor. They are worthless.
A 220A alternator should be plenty for your batteries and system.
I suspect that the rear battery does not have a good enough ground.
This could be because the grounding point of the battery has too much resistance (compared to the battery in the front). OR
You don't have the correct wire gauge to the rear battery from the isolator.
Think of it this way.
With the car running the alternator is producing around 14.4VDC and can supply 220A of current.
BOTH batteries should be charging equally, Voltage wise (although the larger battery in the rear will take longer to reach it's full current potential).
Do the "big three" upgrade and check the resistance of the grounds between the two batteries.
I will bet this takes care of your problem.
A 220A alternator should be plenty for your batteries and system.
I suspect that the rear battery does not have a good enough ground.
This could be because the grounding point of the battery has too much resistance (compared to the battery in the front). OR
You don't have the correct wire gauge to the rear battery from the isolator.
Think of it this way.
With the car running the alternator is producing around 14.4VDC and can supply 220A of current.
BOTH batteries should be charging equally, Voltage wise (although the larger battery in the rear will take longer to reach it's full current potential).
Do the "big three" upgrade and check the resistance of the grounds between the two batteries.
I will bet this takes care of your problem.