Hope this helps some people. My np246 had pump rub and sprung a leak. This is on a 2004 z71 suburban . I didn’t think it was to bad as I can get a new case at the pick and pull yard for $75+ $25 core. Went and got a new one last weekend and took it apart and put a case saver in it. I didn’t fully rebuild it as this is my beater and everything inside looked fresh. Today I pulled mine out and that is where a fatal error was found. There are different encoder motor shafts on different years/models. Mine has a splined shaft and the motor has a 7pin connector. The one from the junk yard looked like a double d steering shaft and had a 4pin connector. I immediately jumped in the interweb and looked for some kind of 7to 4 pin adapter which I wasn’t able to find and it seems as others have had this issue. So it dawned on me to see if I could just switch the motor shafts out for one another, which you can. Be careful as there are needle bearings around the shaft. After that I put it all back together and stumbled onto the next issue. The main input output shaft that has the clutches wasn’t sitting all the way down causing the rear case half to sit high so I took it all apart again and realized the next issue. Which ever motor shaft you use you have to use the same arm that rides on that shaft because the bearing part is set differently on the are(see picture).
This next picture is the shaft I have been talking about. It corresponds with the arm on the top of the above picture.

I have yet to put the case in my truck and road test it so it may not work but it does shift through everything properly on the bench.i would also add I probably took apart and put back together 10times trying to figure this all out, so you don’t have to. I will post again when road tested. Hope this helps someone else and I hope I wrote this in an easily understandable way.
I have yet to put the case in my truck and road test it so it may not work but it does shift through everything properly on the bench.i would also add I probably took apart and put back together 10times trying to figure this all out, so you don’t have to. I will post again when road tested. Hope this helps someone else and I hope I wrote this in an easily understandable way.