... others who have done this mod, ie dual cases, have used the NP231 which doesnt have the highway 4wd mode, so shaft vibrations may not have reared their head
Nope, if anyone tells you this that's BS. Even with the crazy angles I'm running with the SAS and the pasted together SYE on the front output of the Mitsu t-case, I could run 55-60 MPH in 4WD on the highway and it was so smooth you couldn't tell it was in 4WD.
I dont see how the pinion could be out, it was OK before I did the transfer case swap.
I have tried it without the front shaft & its all good. Ive also tried it without the rear & it still gives the vibes.
No worries. It doesn't take much; sometimes all it takes is a bushing or mount sagging a little or loosening up to through everything off. In your case, since you're running IFS in the front, that's unlikely.
Ok. That means that the problem is in the front drive line. That narrows it down.
... One of the things to come out of having the angles measured is that that because I had to clock the transfer case upwards a bit to clear the front torsion bar, that has got the front yoke pointing upwards at 5.5 deg. It then meets a downward pointing drive shaft of 3.4 degs, so that operating angle is 8.9 degrees.
Ok, so ... you did what I got away from by running the split drive shaft. My front output yoke points up, too, but with the split drive shaft, by the time I'm to the CV, its flat with the frame.
5.5 degrees upward at the front output yoke, then downwards 3.4 degrees to the differential pinion. And, you have a CV at the transfer case and a U-joint at the differential. Starts about 80KPH and its an existing problem since the conversion.
Now, I have a question. How does the pinion, u-joint and CV line up? This isn't a u-joint/u-joint setup. The pinion should be in align with the drive shaft. You should be able to draw a straight line through the pinion, u-joint and drive shaft. The angle in a CV setup is handled by the CV, not the u-joint.
If you clocked the t-case either clockwise or counter clockwise from EXACTLY the OEM t-case output location, then the pinion is out of align. That means you would need to do one of two things.
1) Rotate the differential until the pinion is lined up with the drive shaft, OR ...
2) Clock the t-case until the pinion is back in align with the drive shaft
#1 is easier.

So the question is, what's the angle between your pinion and drive shaft? 'cause in IFS, that should be zero.
<edit> No, actually I think zero is incorrect. I think that should be +1 or MAYBE +2 degrees.
Neither CV or u-joints are too picky, and neither is the CV/u-joint setup. Until you start trying to do what you're doing. IME, 50 MPH is about where things start showing up if things aren't quite in align just right.
Edward