Sounds as if you tried a lot not to lose anything around upscaling. Really good is, that you exported from GPVE to lossless images, to collect these together afterwards. How well does the heart of this, GP Video Enhance, seem to work for you? I found it rather weak. Can you post some screens?

May I admit some things? I feel free to do so, maybe I can help:

For IVTC, one of the key points in your workflow, there are much better ways. Most avisynth-experts use TIVTC which produces excellent results without any loss in quality if you use avisynth correctly. Even better is to IVTC by hand with avisynth (even if the doom-cracks don’t like this… 😉 ) Very often you have only one, or less than 4 or 5 pattern-changings to remove, which is by hand done quite fast, and you get 100% jitter-free results, which NO automatic algorithm can achieve.
Also, unfortunately, if telecining (pulldown) had been done directly while scanning and later different compressions were made, there often remain “staircase”-artefacts (don’t know the right term in English) after IVTC. Hard to correct these without losing resolution, but if you plan to upscale/sharpen afterwards, often better to remove it at the cost of a bit less resolution, which you “get back” (not really) with your upscale. Otherwise these staircases will be more and more visible. If you have a source with absolutely NO such artefacts after IVTC, you are lucky.

At the end I would rather export to some lossless codec, then it is possible to later improve something, edit something a. s.o. But maybe you just didn’t mention it.