Well..... I got an update from Standard Transmission and Gear today. Trans and Transfer case will be back in tomorrow morning and test driven after a very speedy turn around. I almost wish I stayed a few more days in the hotel but I told them no rush take as long as you need, but it needs to be done with 100% confidence and understanding as to what went wrong; and what's being done differently to rectify the issues observed.
I've got to laugh else I'll go sane....
Transmission Tear down (no pictures because nothing is destroyed)
3rd 4th and 5th synchro's are being replaced. The ones that came out are just fine. The engagement teeth on those gears are perfectly sharp even with that horrid grinding. The most likely cause of the grinding in those gears primarily 3rd and 4th in the up shifts and double clutch down shifts is too much fluid. The 3rd and 4th gear selection ring/collar are on the counter shaft which is underneath the main shaft. This means that majority of the counter shaft was nearly submerged or completely submerged in oil. The synchro's weren't catching because of the excess fluid, and the temperature of the fluid. The fluid took hours to heat up with my coolers (more on this later). I hope none of you have to know the pleasure of what the synchro's feel like, but if you look at the pictures I posted earlier. They look to have a fine texture ( I believe when new, versus more coarse with wear near the edges of the rings) They feel that way too, and they catch using friction. With the amount of oil in there and at the temperature it was, there was little to no friction which is why there isn't any damage.
Here is a picture of the gear assembly for visuals Counter shaft is on the left, main shaft is on the right.
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There were 9 quarts of oil in this transmission at STGs request when I called over the phone giving details on my prior setup and running conditions before the first rebuild. There were 9 quarts in the transmission because I told STG I had fluid coolers on my trans and my new fill capacity was 7 quarts. This was calculated by me knowing the capacity the fluid coolers added. Those being the Trans cool coolers sold by Genos. Two coolers increase your oil holding capacity by 1 quart. 1 cooler adds half a quart because they aren't hallow and have cooling fins on the inside taking up space and transferring more heat.
The miscommunication between what I told them and what they understood was that STG assumed I was running the Fast Coolers instead of the Transcool coolers. The fast coolers are completely hollow each individual cooler holding 1 quart. Two Fast Coolers giving you an additional 2 quart capacity of fluid. This is where the recommendation for 9 quarts instead of my correctly calculated 7 quarts came from. I didn't think anything of this or question it because im talking to the experts on these transmissions.
Why was I running 7 Quarts with the two Transcool Coolers?
Here is the math.
OEM Stock oil fill amount for an NV5600 (4x4 or 4x2) is 9.5pints which is 4.75 quarts. 5 quarts rounded.
Trans cool Dual coolers added 1 quart total to the fluid capacity. So we now need 5.75 quarts to be at the stock fill level or 6 quarts rounded
I do a 1 quart over fill as widely recommended and needed on both the G56 and NV56 transmissions. We are now up to 6.75 quarts calculated, 7 quarts rounded.
I've been running 7 quarts of oil on this transmission with the stock single disk and dual coolers no problem.
9 quarts of oil is nearly double the stock trans fill amount. Keep in mind the more fluid you have the longer it takes to heat up. Just as it takes longer to boil a pot of water compared to a table spoon.
My 1100mi drive down there further confirms this with my transmission temperature gauge. It took me hours to get my transmission up too operating temp at highway speeds. My operational temp was from 180-190 * Fahrenheit, I stayed around 130 - 160 within the first 8 or so hours of the trip. My oil capacity was too high, and the transmission coolers were too effective at that capacity.
Transfer case Tear down (No pictures, because there is no damage internally)
Transfer case was split open and disassembled for inspection and reassembled. Nothing internally damaged or out of round from whatever happened in the back of R&L Carriers' party bus.
Summary and Conclusion
Final confirmation that the oil amount was the root cause of my shifting issues is pending on the test drives they preform after re-installing the Transmission and Transfer-case. I was told the synchro's that were installed on the first rebuild will be kept for me examine. I'll post pictures of those undamaged synchro's compared to the old ones prior to the rebuild.
This is a very simple lesson in fluid dynamics. The amount of fluid matters and the temperature of the fluid is critical. You can be too cool. Luckily for me there was no damage inside the transmission because everything was so coated and cold. Other systems may not be as durable. i.e. differentials, Automatic trans with heat exchangers removed and deeper pans, power steering systems, oil coolers, lower engine temp thermostats.
If anyone frequents the YouTube channel
Watch Wes Work, you might have seen his video on the hierarchy of reliability. The most reliable to the least reliable in this order. Mechanical, Hydraulic, Electrical, and finally the least reliable Human operator. The miscommunication between two humans about the components the transmission was equipped with lead to an improper amount of fluid being used inside the transmission potentially being the sole cause of the shifting issue in the transmission.
Attention: TDR Forum Junkies 
