the 2zzge timing marks are not supposed to be parallel, it’s all good. I turned the engine until orange chain links were aligned with the exhaust sprocket and intake gear. All timing marks were accurate.No at zero timing mark on the crank those dots should be strain across parallel, if you like, to the rocker cover face. Use a straight edged measurement device.
Did you hear one of the cams skip? , would have been an unexpected ‘bang’ sound