Yup, pulled the engine again. Enlisted the wife's helping hands when needed. Pulled apart the flexplate assembly to see what I couldn't see.
I thought painting parts may have gotten in the way of a flush fit so I started cleaning off paint from the mounting surfaces and found the surface of the crankshaft flexplate hub to not be so flat. You can see the shiny part is the surface that was contacting the back of the flexplate. In fact it may have been part of the reason why my last flexplate cracked the way it did. My close source with a lathe was out of town so I backyard-milled it. I put a sanding disk on my angle grinder and smoothed out the surface. I checked with a caliper to get it even all the way around and worked the high spots to match the low spots. It's not perfect but it's definitely better than what I started with.
Next I noticed the backside of this hub had an indentation near one of the bolt holes (12 o'clock on the below pic).
There was matching metal debris on the surface of the crankshaft. I figure this did not let the hub sit flat against the surface of the crankshaft and caused some wobble in the flexplate/torque converter assembly.
I grabbed a fine file and carefully smoothed off that debris. I sanded the surface after I removed that debris. I also replaced the main seal one more time just in case to eliminate it from being the cause of having to pull the engine in the near future.
I removed the tranny adapter and cleaned out the threads in all the bolt holes that hold it to the block. I sanded the block surface and the adapter surface to remove any dings or potential debris. I then installed the adapter back on and looked for flexplate contact. I did find some new marks. The starter ring looks like it was just slightly contacting the adapter. In the pic below just to the left of the two large bolt heads there is a machined groove. In the center of that groove, the streak, was one set of contact points.
At the bottom of the adapter is another set of contact points. Not all the these points at the bottom are from this round of contact, I had previous contact at some point before I owned this engine when the #4 thrust bearing on the crankshaft failed. The top marks were from the wave ring's bolt heads and the bottom marks were from the starter gear ring. In this round you can see the streak that look darker or dirty and this is the second contact points I was getting. This contact was making the loud "engine" noise I was hearing. With the new flexplate being flat that reduced the clearance behind it and the adapter plate so once things settled out (I'm guessing heat cycling of the assembly and the torque converter) there was no clearance. Plus I found evidence above that the assembly may not have been perfectly flush causing a wobble and that wobble contacting the adapter.
To give myself a more clearance I cut the grooves in both places a little deeper. I did this with my trusty angle grinder.
I inspected the flexplate and wave ring and found no issues. I wanted to build a stronger wave ring (spaces the flexplate and the torque converter mounting points) but I was not able to find someone who could cut out some precision parts I needed to build one the weekend I had time to do all this work so I ended up reusing my wave ring. Cummins wanted a ridiculous amount for a new one (they call it a torque converter adapter) which also drove me to reusing the one I have. I assembled all parts about 180 degrees from last time in attempts to better balance the system.
While the engine was out I found a brake line going to the front circuit getting smashed so I fixed that. I also found the plugs on my fuel pre-filter head , the ones I wasn't using, to be loose. I'm pretty sure I was drawing air into the injection system because of this so I fixed those too. There were times after a hard acceleration and a quick release of the throttle that the engine would die and the injectors would require re-bleeding to get the engine fired up again. I checked everything on the injection pump but couldn't figure out where the air was getting in, this was it.
Once it was all back together and after that nervous first start to see if the noise was gone all was well and that loud noise was gone. Now it's just normal obnoxious cummins noise

. It was a head scratcher why it took a week for that noise to show up but I was glad that all the work made it go away.
We headed to the coast last weekend pulling the trailer with bikes for some camping and riding. It did seem to run a little warm, averaged 205F, but I never got over 220F on the hill climbs. Probably have some bubbles in the system still. I did moderate on the hills because I noticed my hose on the small turbo's outlet starting to degrade so I keep boost below 40psi on the hill climbs. I have a fix for that I just haven't done yet; I need to order a part to finish it. Anyways, it's great to have it on the road again and enjoying that diesel torque. I'm hoping to get back to working on my rear storage drawers and wiring for my fridge.