Do not put multiple game captures and display captures in the same scene, it reduces performance. You've got a scene here or there that have both a game capture and a display capture. This is generally discouraged.
You are getting lag but not an insurmountable amount:
19:41:11.281: Output 'simple_file_output': Number of lagged frames due to rendering lag/stalls: 11 (1.7%)
19:41:11.281: ==== Recording Stop ================================================
19:41:11.298: Video stopped, number of skipped frames due to encoding lag: 36/640 (5.6%)
The rendering lag means that sometimes when OBS wants to render a frame, it can't because the GPU is busy running your game. Usual remedy for this is to cap the framerate in game. I don't know if you've done that already. You say you're already on lowest settings, so there may not be anything to do there if you've already capped.
You're also overloading the encoder a bit, which suggests that it just can't do 720p60. I don't know if there are any other adjustments you can make to the AMF settings to reduce the overload. You might want to try using a slightly smaller canvas size and then scaling up the output to 720p.
