So here it is. My latest workflow. I am a little overwhelmed just how much it has evolved over the last year. Feel free to comment.

1. Using my Canon Vixia HV40, I shoot in 30p mode and capture via the HDMI out onto an Atomos Ninja in ProRes HQ because, well, I can. But seriously, a light touch is always best, I have learned. After struggling all last year with over exposure and peaking, I finally broke down and invested in a lens hood and ND filter kit. It will take some trial and error to perfect things like ETTR, but I am optimistic.
2. Audio is captured separately using my Zoom H4n. I won't be going into any details on the DAW workflow.
3. After ingesting my video, I bring it into After Effects and apply color grading, sharpening, noise reduction, etc. Unfortunately for me, my consumer camera circuitry is quite noisy. Just a fact of life I have to live with.
4. I dynamically link my AE comp to Premiere Pro. PPro doesn't play smoothly a linked comp that has heavy effects. But through the use of proxies I am able to still smoothly edit.
5. Frameserve out of PP using DebugmodeFrameserver in a YUY2 format
6. Load signpost into Avisynth
7. Encode using x264
8. Mux the .264 video and .aac audio using MP4Box.

So far it is the smoothest workflow I have found for several reasons:
1. Dynamically linking AE comps in PP saves me the step of rendering out of AE.
2. I don't need to generate intermediate codecs for editing.
3. This workflow results in two files only, the master ProRes HQ file and the final encoded mp4. All the "intermediate files" are merely AE and PP project files.
4. Frameserving out of PP versus using AME allows me to leverage x264 which I prefer.

Cheers