Bummer that you can't get the VK to work for you without the pricey standalone management. Sounds like you're running into the same issues I've heard of with VK swaps over here, too ... one has to use the same motor, trans, and computers (ECU, TCM, BCM) from the donor vehicle, otherwise the NATS (Nissan anti-theft that you mentioned) gets out of whack. There have been a few VK swaps on the Frontier site, and one Xterra running a VK (Project X2 ... only 2nd Gen Xterra I know of to do it, Stateside, though many talk about it) ... but that one almost shouldn't count, as I believe it was a Nissan Corporate project; or at least had some direct connection to Nissan.
There was also a sand car (2wd purpose built buggy) that had a VK for power, along with a sequential Mendeola transaxle, but I think he was running a custom JWT standalone computer originally built for a VH45 (and modified from there) ... and he also went to a custom Extrudabody ITB setup over the standard VK intake, manifold and throttle body. There have to be some guys out there who run the VK as a drift car powerplant, in Zs and other chassis (heck for the right cash, you can get built long and short blocks for the VK ... somebody must think there's a market); so it makes me wonder what they do to run that motor ... it can't be that everyone who wants to run the VK is doing so with a completely custom standalone setup *OR* every single gosh-darn thing from the same donor - there has to be some middle ground I would think.
I, too, would like to get my hands on a TD42t Y61 ... assuming of course that I could convince myself that parts availability and maintenance support wouldn't be an issue (due to rarity) here in the states. The other option would be to go nuts on a R51 V8 Pathfinder, but someone needs to give me a blank check for that project to be a reality.