I was going to answer earlier but I cannot say 100%. As far as I know (and I have owned quite a few Yamaha's in the past and even currently, including a 1978 DT175 (CDI) and 1978 DT250 (Points), the ignitions system on these bikes are seperate from the charging/lighting system. They can run with no battery and the ignition switch is just a continuation to ground for the CDI/Points. Putting a charger on the battery will not affect the CDI/Ignition at all and won't affect anything unless you turn on the key with the charger hooked up and running. The CDI's rarely die, but that is rarely...I have witnessed one that took a dump.
The battery acts like a big energy sink, thus if you overcharge it, it disposes of the excess current by way of heat (thus boiling the battery).
Check your grounds, ignition switch, spark plug cap, kill switch, even a bad pickup in the case will end your sparking days. It is a simple system, make sure each component is doing its job.