given the fact the bikes came from the factory with functioning ABS that worked with a lead acid battery with no problems, the capacitor addition is a crutch that is hiding the real problem. capacitors should NOT be needed for a functioning ABS. ABS works just fine on the K1100RS in my garage with no capacitors. that fact that is is working in this case shows there is still a bad battery, or more likely one or many dirty connections in the system that are causing a large voltage drop.
problem not solved....keep digging for why the voltage drop is there. when found, delete the extra capacitor thing....