Updating this thread.
Turns out it was a flywheel that had worked itself loose. No so loose you could feel it by hand but loose enough that it would happen under load.
I pulled the transmission again last Sunday with the intention of inspecting the flywheel and clutch assembly as the flywheel was literally the only common part in the different stages of this adventure.
With the transmission out I checked the flywheel for looseness but it seemed completely tight. I removed it anyway and inspected the crankshaft and pilot bearing. They were good. So I reinstalled and retorqued the flywheel and clutch assembly. Put the car back together and figured I hadn't fixed anything.
Drove it today for the first time and to my surprise the problem is completely gone. So apparently it was the flywheel being ever so slightly loose.
Man that took forever to figure out but at least it's done now.
At this point I can proceed on this build. Ordered Brembos for the front and am going to be getting the Vorshlag Bilstein shock/spring camber plate kit ordered this week.
Signed up for an Autocross March 19th and will be able to take this car as planned instead of my 2015 as a backup. Happy about that.