Bike isnt charging battery
If the battery charged before the "chop job/ignition bypass" and afterward does not, the you have left out a circuit that excites the alternator field. This was most likely part of the original ignition wiring, and you will need a Honda wiring diagram of you bike model and specific year in order to identify the wiring correctly. Otherwise, restore the original ignition wiring and switches, and see if the battery starts charging again. Then work backwards removing only the wiring that you know is not part of the charging system. Through the process of elimination you will discover which wire powers the alternator. It will take time and patience.
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