If you are interested in the upscaling, just try pluggin your lossless file straight into video enhancer and skip handbraker or whatever. Because you’ll be compressing to H.264 as you upscale, with video enhancer 2.
or if final cut will let you upscale on export, that would be cool. upscale to lossless, then compress afterward.
scroll up to see my most recent comparison post, with Goldeneye source.