I definitely see your point about being leery of a "rebuilt" transmission. This post had some worthwhile comments about the potentially questionable quality of some rebuilds. And $3K is big bucks.
I wonder if there are any other members who have had an NV5600 rebuilt by Standard? Did the seller mention any kind of warranty? The fact it was rebuilt begs the question "why?". And "how well?". And "what exactly was replaced?" Answers you'll likely never know, except the "how well?" if you buy it.
Mine was from a salvage yard @ 100 miles away. It took 4 phone calls to locate. I got the flywheel and throwout bearing, etc with it (they cut the shifter handle and crossmember to remove it!!#@$%!). The flywheel is absolutely mint. I took that as a small but good indication it wasn't abused. The truck had very low miles. Everything turned and shifted OK. They also gave me a 90 day money-back warranty, which did me little good since I was a long way from installing it, but it did speak well of their confidence in it since they didn't know that. I paid $2K for it. They were also willing to give me $200 back for my NV4500 as a core. I declined politely. I did not know if I needed a different block adapter, so I snagged one for $50 on ebay. Another $12 got me the starter spacer.
I bought a darned-near-new stock LUK clutch (still has clear print on the disc face and virgin machining marks on the p. plate) for $180 shipped from a guy who immediately bombed his new truck after buying it and upgraded to a SBC. Later, I came across a complete, brand new SBC OFE kit for $500 and upgraded myself (anyone want the LUK?). The crossmember cost me $75 with shipping. After buying the wrong (G56) shifter handle by mistake, I came up with the right one with knob for $20 (anybody need a G56 shifter handle & knob?). A complete bolt kit was pricey at $34, but saved alot of guesswork and searching.
So I've done OK on the parts prices, I think, but it all adds up and takes time. CumminsPower98 installed a drain plug when he did his conversion, and I want to try that, too. I also plan to upgrade from the good SBC pilot bearing to the even better one that Dan offers as well the external filters.
A shifter relocation bracket for the t-case, an extended shifter rod (which I can just make), a new transmission mount and mount plate, and a wiring extension harness I think will finish the list. I have no idea what those items will cost. Then I still have to pay for driveshaft lengthening & shortening and many quarts of expensive Castrol Syntorque oil. Does it ever end?
If all of that (minus the oil and driveshaft mods) is what your seller says is a "complete" kit, the 3K, especially if it has a SBC clutch, is a reasonable deal. It's still a lot of money... But so is the cost of rebuilding an automatic or having the NV4500 rebuilt and upgraded right. Tough decision, my friend.
(Please post the link to the G56 info you relocated)