Carb Tuning

So my latest wheeler is a 04 Yamaha Bruin 350. It had all the wires cut from the stator and a few others and no wiring harnesses. The previous owner had them all twisted together and the bike neutral light would come on it would start (hard to start) but then would idle fine. It would die when you gave it gas so I soldered all the wires together and went on inspecting assuming it was a carb issue. Later after the carb was cleaned and adjusted I got this (see video). The bike would want to die anytime you gave it gas and there would be this horrible knocking sound but only when you gave it gas. I was worried it was the rod bearing and electrical still messed up somehow.
Upon further inspection of the wires coming from the stator there was a W/R wired to R and a R wired to W/R. I switched them so they matched per the service manual (W/R to W/R and R to R) and the bike started right up, idled and revved out fine and the knocking noise disappeared. This was the problem the whole time. It was just really hard to tell bc the oem wires coming from the stator were so brown and dirty I could barely make out which was which.
Where the hell did that knocking noise go? and what was causing it?? Just racking my brain trying to figure out what it was so I know for next time but I can't make sense of it... Really thought it was the rod bearing but it didn't make the noise at idle so I was questioning it...Luckily I kept searching!!

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