Thanks for putting the time into the write up that you have done here. I came across your build thread as I am researching fuel pump options or my FG. By chance it happens that we had an exchange relating to the idle issue in another thread.
I have read your entire build thread now and have had similar issues with a Mal Wood option 5 twin plate install. It is not an issue with the quality of the kit, it has now been in my car with a Borg Warner EFR 9180 for a couple of years no issue. Lighter than stock as well. I am not overly hard on it though.
My flywheel bolts loosened off within about 50km of driving the day I installed it, turns out I torqued to factory specifications which was a mistake. Same story as you, was able to redeem the crank mating face with minor filing to tidy up. This was a long time ago (say 5 years) but I think I ended up torquing to around 70-75ft/lb. I think you mentioned 85nm in your post earlier. When the replacement set of arp bolts arrived they came with a little piece of paper that had the recommended torque on it. The first set that came with the kit did not.
Your story was identical right down to forgetting the sandwich plate, thinking it was a bleeding issue, heat issue of the clutch line running near the turbo dump.... Word of caution make sure you check with Mal Wood what torque he recommends before driving her again.