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NV5600 lock up?

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I was towing a boat/trailer < 5000 lbs on my return trip NJ to Atlanta down I-81 and midway on trip a puff of smoke came up thru my shift boot (console still removed to replace heater core AGAIN) and seems like I felt motor being dragged down. I headed for exit ramp in < 2 miles and as I turned on the local hwy and rolled into hotel access across exit, it killed the motor like something froze up. 2 years ago the trans was rebuilt along with transfer case at 200k by local reputable manual only trans rebuilder in Marietta, Ga. They don't take them out, you have to bring trans to them. Supposedly, the trans had been rebuilt but they left out a shim and everything was toast so was a "complete rebuild". Of course its been just over 2 years and put less than 15k on it, so no warranty, mostly non towing although last year towed an 8500 trailer/boat from south Florida to northern Ontario no problems. The truck has 220k on it now and my son installed the rebuilt trans, transfer case, new clutch and pressure plate, etc back after rebuild and it has performed flawlessly. Put in the recommended Amsoil after rebuild and there have been no leaks. Called my son to discuss problem and he said try to bump the started in gear (we've deleted the clutch override safety switch) but the starter acted like it was trying to turn over but something was still locked up preventing it from turning over. After 3 hour cool down (even tho temp was 90+ outside) I tried bumping the starter again and it started. Before I couldn't even shift it into neutral. Now, it started and was able to idle over to proper parking space and clutch was working properly. Bottom line, I paid son's roommate to haul my '99 up to haul boat back and haul my '04 back home to evaluate. We were able to drive it up on the 2 car trailer to tow home and back off. Any thoughts? As I said, there is no indication of a trans leak. Could there be a manufacturing defect in a main trans bearing to get hot and drag down engine/trans until it cooled off? I know these trans get hot and I notice a little more difficulty getting into 2nd after a toll booth stop when they are hot on a long trip. Should I have installed a trans cooler? If that is needed why didn't the factory install one????? Truck is sitting because I don't have another $4500 I can spare for another rebuild. Maybe should send to Standard Gear and Trans in Texas like I did my NV4500 in my '99 to have rebuilt and 5th gear pinned. I don't think I can drop this one out on my trans jack in the driveway like we did with the NV4500. My son borrowed his friends lift to remove and install the NV5600 but its tied up for a while. So trying to get suggestions while I try to locate a shop/lift I can borrow/rent to pull trans to have inspected.
 
With the trans the most you can do with it in is verify operation and change fluid unfortunately. Start with the slave cylinder and clutch would be my recommendation. Will the trans let you double clutch?

In my experience they shift better warm or at temp. I run dual transcool coolers with a Trans temp gauge and im overfilling the trans to the recommended ratio combined with the added quart capacity of the coolers.

Operational temp is usually 190* to 200*. I takes hours to get up to that temp empty for me, most of the time the needle doesn't bump 100, i'll maybe hit 130* on a 60-70 mile round trip. All these numbers are empty.
 
An overheated slipping clutch comes to mind here as another possibility. Including a pilot bearing locking up. Cooling down helps it work again but damage has been done if that’s the cause.
 
The NV5600 has known bearing lube issues that Standard Transmission has developed a mod to resolve. It's covered in this TDR article by Joe Donnelly.

https://blog.genosgarage.com/wordpress1/wp-content/uploads/2012/05/TDR67_MyNV5600.pdf
Reading that article seems to summarize what exactly happened to me, felt the engine being dragged down, immediately slowed and found exit in 2 miles, trans locked up at base of exit, let cool down after 3 hours and was able to move truck. We put 7 quarts of the recommended AMSOIL after rebuild but I guess there are lubrication issues that need attention per this article and that Standard Trans has developed.
 
Drain the oil and inspect it. Black/burnt, or low. If it is low, check your t-case, it is probably overfull. From your description, the transmission will need to come out and be rebuilt.

Do this and report back.

3 quarts overfull will destroy the rear main shaft seal and dump the oil into the t-case.

That, or the rebuild was sub par. They don't smoke and seize up for no reason.

They don't need coolers, keep the oil fresh and full, not overfull.

370k on my '01, standard fill, heavy loads with an extra 120hp, changed every 36k.
 
I will report back what I find. I'm probably going to ship it to Standard Transmission and Gear in Fort Worth if they will take it. They did my NV4500 pinning the 5th gear and rebuilt it on my '99. That shipping cost me $238 after I palletized it and took it to Conway which a shipping expediter found for me nearby (24 miles). I've got to ask a friend if I can rent his lift to pull and drain and store my truck there while its rebuilt. I feel relieved to confirm that this has happened to others but I also feel for all of you at what you've gone thru to find the problem with the very expensive repair and relate it here.
 
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