So after more reading, more researching and more playing I have decided to go with "plan B" which is exactly what Cebby Suggested (Thanks), run the existing gearbox, and use a Suprastick to control it.
There is no way I am going to get my transfer case mated to the A650E without very expensive custom output shaft and casing adapter.
This is a bit of a shame as I like the 5 speed ratios, and it would have been nice just to use factory management to control engine and gearbox, but I don't think the enormous cost and effort is worth the minimal gain. I also learnt that the A6560E are also not as tough as the old A340, and have heard from an expert that they are not great off road as they have been prone to oilstarvation at large angles.
My next concern was that I had also read that the VVTi 1UZ on stock management throws a fit if it can't detect a gearbox, and won't rev properly. I decided to test this and disconnected the autobox controls on my LS400 and tried to see if I can hit the redline, in 1st. The engine revs and pulls as it should. (Private road, obviously, you need a really suprising amount of space to redline a stock LS400 in 1st!
Fot the sake of "search" if anyone is interested, the ratios between the two are:
4 speed Gearbox - A340E (30-40LE) - Also A340F (stock Hilux)
Ratios 1st:2.804 , 2nd:1.531 , 3rd:1 , 4th:0.705, Reverse: 2.393
1998-2000 Lexus LS 400
5 speed Gearbox - A650E
Gear Ratios: 1st 3.357 2nd 2.180 3rd 1.424 4th 1.000 5th 0.753 Reverse 3.431
Yeah, I'll need to sort out my 3.58 Final drive

I calculated that with the diesel final drive (A02B), I am theoreticly geared to hit 233mph at 6000RPM on 33s lol