More diagnostic time today, some learnings:
First, the transmission shifter has 6 positions as well know for P-R-N-D-2-1. The transmission selector shaft has 7 detents! I know the rearmost detent on the selector shaft is confirmed P and from there I can prove out R-N-D, but that's all I've done so far given all of my other issues. In R my back up lights come on, for what that is worth. My B&M shifter cable adjustment is set correctly for P and does give me correct functioning for R-N-D, but it will not go down to 2 or 1 when attached to the transmission, no matter if I try to trigger or otherwise fiddle with it. However, if I disengage the cable from the transmission, the shifter will get back to the 2 and 1 positions. The B&M directions say to set for N and that should get you the rest of the positions, will try that next but that's the lease of my problems.
Next, a fully drained 42RLE system takes over 9 quarts to refill if you added a Rubicrawler and Derale cooler. Mine took about 9.5. Wow, that's more than double the capacity of the transmission alone. I wasted a lot of time and trials sneaking up on that by checking the dipstick after adding more a 1/2 quart more fluid but before it settled enough to give me a "clean" reading. Once I got the right amount of fluid, I got my gear engagement. I've still got a little grinding noise getting back into park from neutral and I can feel it directly on the selector shaft. I hope that settles down over time but I did cycle the transmission with far too low a fluid fill during my attempts to fill it, so hopefully no damage done.
Also, I damaged my transmission fluid gage and need a new one, ordered. I confirmed I've got power and group but I had previously accidently put 12V on the probe tab, now reading the manual that will damage the unit.
Finally, my transfer case appears to be "eff'd". At worst I've got only 2H working and at best I can sometimes get 4L to engage. I've got two neutrals, so no 4H. Shifting between positions is very hard and not always possible without some cycling of the transmission. Note all of this is being done up on a lift, so no real load on anything and I know it is often needed to jostle a Wrangler into or out of 4L, but not sure that is my situation, especially with a cable shifter. Note that before I put the TC in the Jeep I was able to confirm functioning of the modes on the bench, and again in the Jeep by turning the driveshafts. Maybe now being driven by the engine and trans, it has failed in some way.
As a recap, along the way from the stock NP231 that I had when I started, I put on a SYE kit and also a wide chain and 6 gear planetary using an upgrade kit off e-bay. The upgrade kit also included a heavy duty 5.5 inch sleeve and mode fork, which I used. Either that is not compatible with my NP231 or I botched the assembly.
I could try to drive it weight on wheels and see if that changes the TC behavior, but I am skeptical. Seems I am now going to have to pull the TC and tear it down and see what may be wrong with it. Damn, so close but now so far from driving this thing.