The UK's Shameless Screen Entertainment released this baby last year on DVD and Bluray, doing superb job on it. Quote from the release information: "Restored film rebuilt with prior missing footage." I have one of these babies in my collection and heavily recommend obtaining one.
"The horror... The horror."
Shell out the money for the German release from Koch if you have it. The picture quality is superior to the UK's Shameless disc and the extra footage is also sourced from a better transfer, making the transitions less jarring. Plus it's a limited edition and the packaging on the thing is just a thing of beauty. You'll be paying about $45 for it, but it's well worth it in my opinion since it's currently the best version of the film on the market.
shareYou finally get your wish, though this is probably overkill for what most would want. I just watched the movie for the first time (streaming on Plex) and while it was good to finally see it, I don't think I want to spring for this much of a deluxe edition.
https://severinfilms.com/products/four-flies-on-grey-velvet-4-disc-4k-uhd-blu-ray-cd-w-slipcover