Hi DeafEyeJedi
Thank you I used your workflow and it worked perfectly, unbelievable how easy it was and considering how I had been battling getting the rendering right in After Effects using the RAWtoMLviewer export, then to import into After Effects and have my frames not render correctly, and I did not even look at sound yet. This is by far the easiest workflow!
To date I have tried three options, the MLviewer/AE method, the MLVtoMovie app and your method which I'm quite happy with

I just have a question on how would you recommend I upscale my footage in that same workflow, I have a 100D and I recorded at 1088 x 278 at 60.006FPS continuous, now the export to .mov works perfectly. BUt I guess I'm such a newb that I still don't know how to get this upscaled within the workflow. Do you have any suggestions?
Thanks again.
Kaves