Eric,
I had the NV-5600 in my '01 rebuilt by Standard Transmission and Gear in Fort Worth, TX about two months ago while waiting for my new truck to be delivered. (My son-in-law and daughter were waiting to purchase the '01 so I had it rebuilt and rebuilt correctly)
I strongly recommend Standard Transmission. They treated me very well and fairly. I delivered the truck to them early one morning and camped out in a nearby cheap motel. The truck was handed back to me at the end of the second day. They had a driver and shop truck run me and my German Shepherd companion back and forth between their shop and the motel. After the transmission was disassembled and vat cleaned they picked me up and brought me back to the shop for a "show and tell" then delivered us back to the motel after the decisions were made. The rebuilder was very knowledgeable and generous with his time slowly explaining and showing me what should be replaced.
My truck had a little over 300k miles at the time with lots of heavy (commercial) towing history. The mainshaft and sixth gear were worn, a large roller bearing assembly was rough, the synchro drum was worn, and the clutch disc and flywheel were hotspotted (3. 54 gears). Standard presented me with several options and I chose to replace everything needed. Then they offered to charge me only for the parts mine needed but immediately install another unit that had just been rebuilt and was sitting on the floor because they understood I was an RV transporter and wanted to get back on the road, not hang around another day waiting for mine to be built. They charged me for a new mainshaft and the case seals at each end of the shaft, the sixth gear, the roller bearing assembly, and the synchro drum plus a new clutch pressure plate and disc, new throwout bearing, and pilot shaft bushing. They only charged me for the parts actually needed for my unit. The price including all parts, labor, fluids, shop miscellaneous charges, was less than $1900. If my transmission had required everything, a complete rebuild, the price would have only been $2450 plus the clutch parts.
Standard gave me a 36 month 36k mile warranty in writing and I left smiling. I pulled trailers for another month or so with it and finally handed it over to my daughter and son-in-law with 322k on the clock. The rebuilt transmission worked like new and actually shifted better than the original one when new.
My understanding was that Standard purchased a large quantity of NV-5600 parts and can continue to rebuild them for the near future. I don't know, they could have run out already. I would call them if I were you. They are TDR advertisers.
You could pull your transmission yourself and ship it to them, have a local shop in your area do the r and r, or simply drive the truck to Fort Worth.
If Standard has the parts I promise you you will not go wrong with them.
Harvey