remux mp4 question: PLEASE HELP

I have an mp4 with subtitles and audio that I want to remove, just keeping the video and the ac3 6 channel English audio. I also want to add a 2 channel AAC audio to the mp4 so I can play on devices that can't decode ac3. The way I was doing it in the past was to:

1.) Open the MP4 with MKVToolnix and remove the files I don't want and save as MKV.
2.) Load the new MKV into Vidcoder and add a second audio, creating the 2 channel AAC file back into an MP4

I know this is not the best way to achieve this so can someone please advise if there is a way to achieve the above without quality loss/re-encoding?

Thanks for your help in advance.