What wattage headlight do you have? What other non-stock electrical loads have you on the bike?
The stock alternator makes a minimum of 150 Watts (Some examples can be more due to production variances). But it is self limiting to never make more power than capable. If you demand more current, then the voltage output reduces. So, likely what is happening is the extra headlight power load is causing a system voltage drop, which is low enough to not really charge the battery.
The stock bike draws about 10 A (120w) with lighting on. This leaves 30 W for battery charge when needed, or 2.3 A for battery charge when revved.
Higher watt headlight, 3 ohm coils and dyna ignition will all rob power from the that 2.3A margin and leave you with none to charge the battery.
Some help can be had by improving the v loss between battery and vreg, as the vreg powers the alternator field with the voltage it gets. The high voltage the stronger the alternator output can be, or restated the lower voltage sent to the field coil, the lower the magnetic field strength, the lower the peak watts output.
To find the connection loss, you place voltmeter leads on either side of the inline component in question while full load is place on the circuit. Resistive elements will show the exact voltage drop across that component. In this way, you can find he max contributor of v loss in the circuit.
Clean contacts are a good first step. But, contact pressure can effect resistivity, as well as contact area of the connection. A clean contact that is half worn will added resistivity. A fuse that doesn't make full end cap contact can also add resistance and voltage drop across the connection.
You do know that the charging system at idle allows only about 1/3 of max alternator output, right? Same rules for volts plus current limits apply.
Cheers,
