The battery is used to power the ignition system, lights and horn so the bike's AC generator (alternator) must produce enough electricity to meet the needs of all these components plus the extra current needed to keep the battery fully charged.
The difficult arises because the demands of the electricity system are variable and largely determined by riding conditions. For instance, significantly more electricity is needed when the bike is at ridden at night since the head and tail light consume a relatively large amount of electricity. Without a mechanism to balance the output of the alternator to the demands of the electrical equipment in use at any one time the battery will be under or overcharged.
The approach adopted by Honda, and other manufacturers at the time, involves separating the alternator output into two: the first part is used to supply sufficient power for the ignition system and occasional use of the turn signals, brake lights and horn; and the second part is enabled when the head and tail light are turned on, providing the additional power needed by the lights.
There is nothing really wrong with the approach, and it was used on millions of bikes back in the 60s and 70s, but it is rather rudimentary and does not cater for all the variable electricity requirements on the bike. For instance, the amount of electricity available to charge the battery changes according to engine speeds and how often the rear brake light, indicators and horn are used. As a result, if you do a lot of stop-start riding the battery might not charge properly and if you do long distances at higher speeds the battery tends to overcharge.
The charging system, and how to improve it, is explained below.
charging system
The charging system is very simple, consisting of an AC generator ('alternator') and a rectifier. The alternator generates alternating current and the rectifier converts this to the DC (direct current) needed to charge the battery.
Alternator
The alternators fitted to these bikes are called permanent magnet alternators and their power output is determined by the physical properties of the components used (the strength of the magnets and their proximity to the coils the number of windings etc) and the speed of the engine. This means that the power output will continue to increase according to the speed of the engine up to the limits of the device.
Rectifier
Prior to the introduction of the K5 model in 1974 the bikes were fitted with selenium rectifiers - easily recognisable due to their bright orange paint (see below). These rectifiers are inefficient and prone to failure (incidentally this is why the rectifier connections on the Honda wiring diagrams are marked "SE"). Honda replaced these with a silicon rectifier in later models.
night time riding mode
As mentioned above, the electrical system is set up to produce extra power when the head and tail lamps are on. As you can see in the illustration of the alternator above, the stator has 6 separate coils. These coils are wired together to form 3 pairs and - as can be seen on the wiring diagram above - one pair of coils is permanently connected to the rectifier by the yellow wire in the wiring harness.
The remaining two pairs of coils are only connected to the rectifier when the lights are on, thus providing extra electrical power needed by the lights. The connection to enable the "booster" coils is made in the horn/light switch: turning on the lights, as well as connecting the head and tail lights into the live battery circuit, also connects the yellow and white alternator output wires together.
In the older manuals, Honda refer to this as 'nighttime mode' and call the two pairs of coils that are added into the circuit by the light switch the 'nighttime coils'.
marginal charging rates
The charging current is the amount of current left over to charge the battery once all the other electrical demands of the bike are satisfied. The standard charging system on the 6v bikes should produce the following charging current:
The first thing to note about the table above is that the alternator does not generate enough power to start charging the battery until around 2800 rpm. In other words when the bike is idling some of the power needed to supply electricity to the bike will come from the battery and it will be discharging. As explained above, the amount of charging current available is also reduced when doing a lot of stop/start riding - since the engine will typically be running at lower average speeds and the indicators and brakes are used more often.
The marginal nature of this set-up can also be effected by maintenance issues, for instance corrosion in the wiring connector can create corrosion that reduces the amount of current available for battery charging.
Unfortunately, where a combination of riding style and poorly maintained electrics prevents the battery from charging reliably this can effect the ignition - which is powered by the battery - causing the bike to run badly or making it difficult to start.
One way to reduce the likelihood of a flat battery would be to use a higher output alternator, but this too can cause problems as Honda found when they started to receive complaints about failing lights and batteries on their early bikes. This problem prompted Honda to introduce new low output alternators in the mid 60s:
regulator
One way to minimise the type of charging issues described above is to use a device called a regulator. Although Honda did not fit them to the CT90s they used them to minimise overcharging problems in other small capacity models of the same era. Here is a 1969 service bulletin about excessive voltage issues with CL-175s:
Honda says the regulator performs thusly
"upon the battery voltage reaching (the target voltage), the regulator begins to actuate in order to bypass a surplus current, reducing the amount of charging current, to prevent the battery from being overcharged"
In other words, when the voltage going to the battery exceeds the preset voltage limit of the device (typically around 7-7.2V for 6V regulators) current from the alternator is temporarily shorted to earth in order to maintain the optimum charging rate for the battery. Since the device keeps the battery charging current within safe limits no matter what the alternator outputs, the balanced charging system described above is no longer needed.
full charging upgrade
The good news is that modern versions of these devices (which combine the regulator and rectifier functions into a single unit) are easy to retrofit to old bikes that only had rectifiers originally.
This is a popular upgrade on Honda twins of this era. A manufacturer that comes highly recommended by the people over at the Vintage Honda Twins forum, Spark Moto, provides a 6v device and this is a version I have fitted to a couple of my bikes, including my CT90.
You most likely need to adapt the connections on your regulator/rectifier to fit the harness connections. In the Spark Moto device the black wire is for voltage sensing and needs to be connected to a wire in the harness that is live when the ignition is turned on (Honda switched battery positive wires are usually black). The red wire goes to the positive battery terminal (via the unfused red/white wire in the CT90 wiring harness); the two yellow wires go to alternator and the green is to earth the device.
After fitting a device like this the output of the alternator is automatically regulated, so it is no longer necessary to retain the old 'nighttime' charging mode and you can use all three pairs of alternator coils all of the time, knowing the modern regulator/rectifier will take care of any excess power.
To enable the 'full charging' mode you simply connect the white/yellow tag and yellow wires in the section of the harness at the headlight. This bypasses the connection made in the light switch.
This improvement will mean that you get full charging all the time - which can be useful where bikes are used infrequently and the battery doesn't get a regular charge - while protecting batteries and light bulbs from the effects of excess power.
As an added bonus the rectifier technology in the modern devices is more efficient than the older rectifiers - particularly the old selenium rectifiers which were never very efficient and deteriorated with age - and this frees up more power for charging.