The Scribbling Man said:
Right now the only issue is working out how to fix the aspect ratio, which must be doable.
Why do you think it must be doable? If the video was incorrectly resized at the Handbrake stage, then that resizing is "baked in". It's possible to resize the video again, of course, but resizing the video and then resizing it back is not a good idea as far as quality is concerned. You'll have two sets of (unnecessary) resizing artifacts.
If you can make a sample of your MP4 and send it to me, I'll try to see if I can work out if it is the source of the problem. At present, there are two stages at which the error might have been introduced, and it's difficult to work out which is the culprit.